Wild Pokémon requiring you to send a Pokémon out every single encounter, in situations where you're just going to run from them anyways. Wild Pokémon encounters are the most basic and trademark part of the game (other than trainer battles), but it can get irritating when you're in an area with pesky high-Speed Pokémon that don't let you run, making you wonder "Why did I have to send out my Pokémon in the first place?!" (Except maybe in HeartGold & SoulSilver, when your lead Pokémon walks by your side.)
Safari Zones. They force you to catch rare and hard-to-catch Pokémon with just Safari Balls (which have the same catch rate as Great Balls), bait, and rocks (or mud). Shiny Pokémon in Safari Zones deserve special mention. They're already incredibly rare, and now they have a chance of running away... WONDERFUL. In Black/White, they didn't bother with one. (Unless you count the Wildlife Preserve, but it doesn't operate like the other Safari Zones. You can use regular balls.)
X/Y replaces the Safari Zone with the vastly superior Friend Safari. You choose a person from your system's Friends List and gain access to an enclosure with tall grass containing two (or three, if the friend has beaten the Elite Four) Pokémon of a specific type based on their Friend Code, all set at level 30, and you fight them like a normal wild encounter. Not only are many of the Pokémon available this way rare, but all of them are guaranteed to have two perfect IV's, there's a chance that the wild Pokémon will have its Hidden Ability, and there's a higher chance of encountering a shiny Pokémon. The two main flaws are that you can only access it after you beat the Elite 4, and that the Pokémon you have access to depends on who you have registered as your friend.
HMs: They're required to make it through the game, but they each take up a move slot and most of them are practically useless in battle. Each use comes with a time-wasting animation and the moves themselves cannot be forgotten until you meet the Move Deleter, who always appears fairly late in the game. In fact, in Generation I there wasn't a Move Deleter at all! If you clumsily taught your Charmander Cut, better be prepared to have your Charizard still have it during the Elite Four battles. What were they thinking?
This used to be justified to some extent, given that since HMs can (in Gen. I) be placed in storage like any other item, a Pokémon could be traded in knowing the move without the player having obtained the HM in the first place, and screen transitions cause trees to regrow after being cut down, boulders to replace themselves after being moved or broken, and so on. They can also create HM Slave(s) to avoid wasting moveslots on their good Pokémon, but that means they don't have 6 good Pokémon with them in caves (where they are often needed most). A player could inadvertently render the game Unwinnable by overwriting a necessary HM move in the wild and leaving himself trapped. Of course, this whole train wreck could have been averted with some Gameplay and Story Segregation.
Black and White attempted to fix this. There are only 6 HMs, and you only need one to progress through the story (ONCE, at the beginning). The others lead to hidden items. Players are now kept in check through extensive railroading. The Strength boulders also permanently stay down instead of resetting themselves as they did with past generations, so you don't have to worry about using Strength again if you go back through an older area. The problem with the trees still exists, though, but now they at least stay cut down for 24 hours before regrowing.
You can't trade a mon that knows an HM to a newer game without going to the Move Deleter. It was a way to keep players from getting stuck, but it's still annoying. No Surfchus in Gen V, because the surfing Pikachu has to forget Surf before you port it.
And this whole annoyance could have been avoided with the implementation of The Legend of Zelda-style items that helped you overcome the obstacles. Ironically, the whole HM mess started out of a misguided attempt to ape the mechanics of the Zelda franchise, which was, then as it is now, extremely popular. There is a Dummied Out item in Pokemon Red And Blue that lets you surf, although it could have just been for debugging. Nothing like this has ever showed up in later games despite the massive outcry against HMs. The annoyance could also have been mitigated if the majority of said moves are something other than Normal-types and thus at least could be exploited for type advantages.
Starting in Generation IV, Surf received a physical counterpart in Waterfall. Now, both Surf and Waterfall are very good moves... however, there's no combat reason for a Pokémon to know both (since one will inevitably outdamage the other). This means in order to climb a waterfall, you'll either have a Pokémon with a completely redundant move, or have to fit the other move onto another Pokémon.
Many Gyms have gimmicks that are borderline Guide Dang It in case you want to get straight to the Leader while avoiding the other Trainers. While this is very hard to do, it is feasible (the Saffron Gym is an example) - but only, as mentioned, if you have a guide handy so you'll know where to go (again, the teleporters in the Saffron Gym are an example; another frustrating one is the Opelucid Gym in Black/White and Black 2/White 2 where you have to step on switches on the dragons' hands so they'll go up or down and, depending on the hands' position, the statue's head will go up or down, enabling you to go where you want - or not). Even if you don't intend to take on the Leader right away, you may find yourself running in circles so often to the point of being frustrating (once again, the Saffron City Gym is guilty of this; first-timers may also have a hard time with the rollercoasters in the Nimbasa Gym).
Pokémon and items which require a rare Pokémon to unlock. You want an Aerodactyl in Gold/Silver/Crystal without calling upon the first generation games? You need to catch a Chansey and trade it to an NPC. The encounter rate for finding Chansey? 1%. And then you have to either breed it or catch another one if you want to add a Blissey to your Pokédex. Generation III made it necessary to catch a Relicanth to get the legendary golems, which - with its 5% encounter rate in a handful of very specific areas - has been known to require 101 consecutive uses of Sweet Scent to actually find. Oh, and if you want a Zorua in Black/White? You have two options: either a) have a fateful encounter Celebi, or b) one of the 3 shiny legendary beasts that were distributed a fairly long time ago. Fortunately, in the sequels, you can get a Zorua from a former Sage that doesn't require any event legendaries.
Losing battles that should have been easy wins through no fault of your own thanks to a critical hit is almost a rite of passage for competitive Pokémon battlers. Since switching is extremely commonplace in those matches, Pokémon will frequently switch onto a resisted hit or one that should deal a survivable amount of damage - only to see the dreaded "A critical hit!" message. If that was the only counter to the opponent's mon? Game over.
Likewise, when one's trying to catch a rare wild Pokémon, then accidentally makes it faint with a critical hit. This especially goes for shiny Pokémon.
Not helped by X and Y's Affection stat. If you max out a Pokémon's Affection, it gains an increased critical hit rate, and all crits are now accompanied by the message "[Pokémon] was so in sync with the trainer's wishes that it scored a critical hit!" Uh, no, I did not want you to faint that shiny Pidgey with a critical hit, thank you very much.
In all fairness, Maxing affection takes a bit of dedication, and there is False Swipe, which cannot knock out a Pokemon. However, if you or the opposing Pokemon automatically starts sandstorms as their ability, it can take that last bit of life down without you planning on it, which is frustrating. The rule of thumb is simply to have your false swipe pokemon at the front of your party and make sure it doesn't cause weather effects.
The Name Rater. Game Freak could've made it as simple as including a name-changing app on whatever personal device you have depending on the region your game takes place in or maybe a function for the PC over at the Pokémon Center. Instead, you have to look for this guy and have him judge whether you can rename your Pokémon or not. He always gives you the option (granted, his occupation would make more sense as a name CHANGER since he never gives you an actual rating for your Pokémon's name) unless the Pokémon was obtained through a trade, migration, or an event. The former two would be somewhat more tolerable if he only reacted this way to the ones that already had names, but this reaction towards event-obtained Pokémon is unacceptable. You aren't even given a side-quest to obtain the Pokémon most of the time like they did with Victini; they just straight-up give it to you. The least they could do there is let you name the Pokémon after the delivery guy gives it to you like any other gift Pokémon you get within the game.
Now in Black and White, all new Pokémon's names are in lowercase (Raichu) so when you have your old Pokémon (RAICHU) from a previous generation, you can't get its name lowercased. If your Pokémon is one that can still evolve, its name will become lowercase once it evolves. This also affects Pokémon from the German, French and Japanese versions: they will lose their respective version names when evolved. Pokémon Bank thankfully fixes the capitalization for Pokémon without nicknames when transferring them up to X/Y.
Game Corners. Some TMs, held items, and Pokémon are only available through these annoying gambling minigames unless you want to spend an obscene amount of money buying all the coins yourself. Made even worse in certain generations where the slot machines are so rigged they'd actually be highly illegal in a real-life casino. If ever there was a legitimate excuse for Save Scumming or even GameSharking, this is it. Black and White finally ditched the concept altogether. Though it was more due to stricter regulations on game content, some found it welcome.
The inability for players to buy Game Corner coins in Pokemon Heart Gold And Soul Silver is this to many. A new minigame called Voltorb Flip allows players to amass coins for free, but rather slowly relative to the number of coins needed to buy anything worthwhile. Factor in the fact that some players don't have the patience to learn how to play Voltorb Flip...
The Storage System in Generation I (changed in subsequent gens). When a box was full, you had to go to a PC and change it manually, not so bad, except it won't let you know when the box is full until you are trying to catch that danged Tauros you spent the last 20 min. looking for.
While not as bad in Generation II, as Bill would call you up if your current box was full, you still had to go to a PC and change it manually. Better hope you're not in an area with a lot of Pokémon you want to catch.
The trading system. For many years, the only way to get Pokémon from other versions is to physically find another player and either player needed a link cable to connect the two Game Boys so they could trade. This wasn't a problem for kids at school since the series grew popular with them and someone was bound to have a link cable, but if you lived in a place where not many people had the games, you were out of luck for 100% Completion. People either opted to own two Game Boys, a link cable, and both versions of the current generation Pokémon games so they can trade with themselves, or went for the cheaper route and got a Gameshark or Action Replay so they can just cheat for the Pokémon they needed and get the event Pokémon that they couldn't get. This trading mechanic is very popular in Japan due to how densely populated most cities and towns are, so it wouldn't be hard for players to meet other players that had the game. Outside of Japan, it is not the same case.
Gift or Event-only Pokémon themselves, too. Want a Celebi? Too bad, they're nigh-unobtainable without cheating or hearing about a giveaway and being in the right place at exactly the right time. Wi-Fi connection events in Gen IV and Gen V fixed it somewhat, but if for some reason you couldn't connect to the Internet on your DS (and even going to a McDonald's wasn't guaranteed to work, as you still might not be close enough to the router), you're screwed.
Made worse by the fact that prior to the DSi and Gen V, most routers and encryption types were not compatible with Nintendo Wi-Fi. So unless you had one of the chosen Wi-Fi routers and your router unsecured or is the easiest encryption to overcome, you still won’t be getting that precious Celebi that you’ve been asking for.
The worst thing about this is that the first event-only Pokémon, Mew, is only such because the developers added it at the last minute and never intended for it to be obtainable, which is why it has no bearing on the Pokédex. There is no valid reason (and no, the Grandfather Clause is not valid) for such unobtainable mons to exist in later generations, making this the Franchise Original Sin.
The Day Care. It raises your Pokémon for you. It sounds good, except your Pokémon will not evolve if they reach their evolutionary level while in the Day Care. The Pokémon you leave in the Day Care can also learn moves, but if they already have 4 moves, one old move will be deleted. Problem is, you don't get to choose which old move gets deleted or if you even want the new move at all, which makes it a huge pain if you're breeding for egg moves. Thankfully, Generation VI won't apply the changes until the Pokémon is removed from the Day Care, so you don't have to withdraw them all the time to rearrange their movesets.
You cannot change the nicknames of traded Pokémon. While this is a decent feature with Pokémon received from friends, it's awful for in-game trades, such as the Farfetch'd in Red and Blue, the ONLY Farfetch'd in both of those games, nicknamed "Dux".
This is especially Face Palm-worthy when the Pokémon in question doesn't even have a nickname to begin with.
This actually makes a bit more sense when you take into account the culture Pokémon was made in. In Japan, it's considered rude and ungrateful to try and modify or meddle around with a gift. Doesn't make it any less frustrating when you're plying the Wonder Trade and keep getting Pokémon named "DICKS" or some such.
The Individual Value (IV) system. Natures are similar, but they're much easier to breed (or soft-reset, in the case of pre-existing encounters) for. IVs are hidden numbers in a Pokémon's data; each stat has a number that that goes from 0 to 31, boosting the Pokémon's stat by up to 31 extra points at level 100. It was meant to make each individual Pokémon more distinct, but in the end, there are many problems. While the series values friendship and working hard as key to success, if your favorite Pokémon has bad IVs, the key to success will be to breed a better one, an extremely convoluted process that involves lots of luck and possibly inbreeding. Unlike Effort Values, you can't do a single thing to change IVs without hacking the game. Do you have a Pokémon that needs to use Hidden Power? Your problems are compounded by several orders of magnitude, especially considering all the math that goes into Hidden Power. Most damningly, the system is bad for legendaries. Why? You can't breed for better ones. It's one of the biggest reasons for the massive amounts of hacking and the popularity of online battle simulators. Some even consider the IV system one of the biggest barriers for players trying to get into competitive play — if your team doesn't have perfect stats, you have no choice but to get out of the competitive scene and go hatch a few hundred more eggs, since only perfection is good enough for competitive play.
Generation VI went some ways into making the system easier to deal with. Holding a Destiny Knot when breeding a Pokémon will transfer five IVs to the offspring. Baby Pokémon, Legendaries, and Pokémon from the Friend Safari will have multiple stats with IVs of 31 when caught (two for Friend Safari, three for Pokémon in the No Eggs/Undiscovered group, most notably Babies and Legendaries). Even more, Hidden Power was changed so its damage value was no longer determined by IVs (but its type still is), being at a flat 60 damage. Some players wanted the system gone completely, but the changes have pacified them for the time being.
Started or Originated in Gen II
Roaming Pokémon. They're legendary, which makes them hard enough to catch on their own. They only show up randomly, and it's often hard to track which route they're on at all, not to mention they often switch randomly. They run at the first opportunity and the standard status effects don't prevent them from fleeing; only trapping them will work, and the trapper must remain in battle. A few running Pokémon even have the move Roar, which instantly forces you out of the battle (and, in FireRed & LeafGreen, at least, prevents you from ever encountering them again). The one upside is that their HP and status don't replenish between encounters. The runners' natures and stats are determined randomly when they start running, not when you catch them so save scumming for one that's actually usable is impossible.
In the third-generation games, with the exception of Emerald, a glitch forces all roamers to have horrible IVs. Although the HP IV is unaffected, the Attack IV maxes out at just seven and the rest of the IVs are all zero. After spending all that time and effort trying to chase and catch the roamers, it's a major kick in the shorts to find out they're far weaker than they should be.
And there's the fact that in FireRed and LeafGreen, if Raikou or Entei use Roar, they're goneforever.
It's not bad in Pokemon Black And White though. Right before your game's respective roamer is introduced into the game's plot, Professor Juniper gives you Chekhov's Gun in the form of a Master Ball. Wherever the roamer may be (be it Tornadus or Thundurus), the marquees at each rest stop will tell you that a storm is going on in that area which will save you the trouble of blindly searching for it.
The easiest way to deal with this is to simply look up the level of the Roamer you want to catch, put a Pokémon at or just below that level at the front of your party, buy a bunch of Repels, then run or surf from route to route on routes below said Pokemon's level. Eventually the roamer will warp to that route and you will encounter it, then just chuck your Master Ball. Tedious, but much less frustrating than hoping to encounter it the normal way.
The fourth generation has two roaming Pokémon (well, there's five in Platinum) but it's a little easier to bear thanks to a feature that allows the player to track roamers on the bottom screen of the DS.
Pokémon X and Y takes away the aggravation of fighting and capturing them, but still makes you hunt them down first. Instead of having you fight them when you stumble across them, they flee before you get to do anything. After encountering them like this a certain number of times, they'll settle down in a fixed location, where you can challenge them (and soft-reset) like normal.
Evolution by happiness. Unlike Level Grinding, trading, or use of a certain item, there's no quick way to evolve a Pokémon by happiness. You have to keep it in the front of your party, battle with it, pile on the items and/or not let it faint. Depending on the game you might be able to feed it Poffins or Pokéblocks, but it can still eat through your supplies very quickly. If you want to make your Pokémon evolve by happiness by next level, then you have no choice but to stick it in the front of your party and go running around, north, south, east and west, for literally thousands of steps. This method will take at least more than three hours. It's bad enough when it's a Pokémon you want to use, but when you just want to get it on the Pokédex it's downright annoying. Plus, since there's no set level for a happiness evolution, if you aren't careful you can potentially lose out on a good move by evolving too early/late.
There are ways to get around it though: Put a Exp. Share on that Pokémon and let the other Pokémon battle for it; equip the Soothe Bell, which doubles the rate of happiness gain; catch the mon by a Luxury Ball, it gains an additional happiness boost on all positive actions as well; or stuff them full of vitamins (Carbos, Proteins, Calcium, etc.) or friendship-raising berries. note However, you have to put up with the side effect of the mon's EVs dropping every time you do it.
Okay, so The Battle Frontier makes for a pretty good side challenge for the competitive gamer and whatnot, but why is grinding Battle Points necessary to get anything? By the time HeartGold and SoulSilver came around, the list of things that could only be bought with BP amounts to TMs, evolution items, training items, held items, and even Move Tutors. It wouldn't be such a bad idea if it DIDN'T TAKEFUCKING FOREVERTO GRINDTHAT MANY POINTS. The only way you'll get a sizable amount in a decent time is to actually get the chance to challenge a Frontier Brain, but even provided you make it to them, they could still easily whoop your ass and ruin your streak without so much as a consolation prize. Apparently, Game Freak thinks only gods deserve to teach their bugs how to bite things or something.note It doesn't help that the shards, the payment for Move Tutors in Platinum, are easier to grind in this game but instead are reserved for berries.
Thank God for the Trainer House in Viridian City in HeartGold and SoulSilver, where you can battle Cal and other Trainers whose Pokéwalkers you interacted with and win 1 BP per victory. Made better by the fact that you can have up to 10 people (plus Cal) and just have them put low-level Pokemon in their teams when they interact with you. You can get up to 11 BP per day this way, which really adds up fast.
Meet Quick Claw Horn Drill, the champion sent by Random Number God to smite those who had the unholy thought of setting some sort of world record at the Battle Frontier.Explanation Quick Claw makes the Pokémon holding it move first in its bracket regardless of Speed 20% of the time (ignoring Trick Room if it's set up). Horn Drill (and similar moves in other types, HD being the most (in)famous) is a One-Hit Kill whose accuracy depends on the level of Pokémon (30 + [user's level - target's level]), automatically failing against Pokémon of a higher level (though they worked differently in Generation I). The game is known to skew hit rates as the streak goes larger. Put two and two together.
The difficulty of racking up Battle Points was finally changed in X and Y, where you get Battle Points after every trainer you beat instead of having to fight through a group of trainers just to receive one measly BP. You can also take breaks without having to resume in the middle of a challenge, and can change up team members if somebody's underperforming instead of having to drag them along for the full seven matches or so.
The level curve in Pokemon Gold And Silver and the remakes, Heart Gold and Soul Silver. In other words, there is this long portion of the game where wild Pokémon are at such a low level that they're not even worth using or training. For basically the entire second part of Johto after you beat Morty, the wild Pokémon are usually high 10s or low 20s, and the trainers aren't very strong, either. They're greatly disproportionate to the tougher fights such as Gym Leaders. To put that in perspective, after beating a Level 38 Houndoom in the Radio Tower in HGSS, then you can go to Route 45, which has wild Pokémon in the mid-20s (though admittedly, the Trainers on that route are slightly higher), and the Ice Path right after has slightly lower levels in fact. Then, in Kanto, the wild Pokémon are at roughly the same levels they were in Generation I and their remakes, with a few exceptions. Your best bet is to hope trainers will call you and want to battle you, or in HGSS hope to be on the right day and get certain trainers to rematch you, and even then that will only get you so far. This makes it very unpleasant to train up a new Pokémon, not to mention in Nuzlocke runs, makes it painful to recover after a death.
The PokéGear and the PokéNav in the Johto games and Emerald. Normally they're phones that allow other trainers you've already battled to call you for rematches or to inform you of Pokémon swarms in certain areas, which is quite nice, except more often than not, they'll call you with some pointless information like how cute their Pokémon are, or they fed their Pokémon some berries and state they ate some themselves and wonder if it's safe for humans, or brag about their Ratattas.
This was partially true for HGSS; but they gave you the option to rematch Gym Leaders with decent leveled pokemon and they removed the limit on who can call you so you have more options available. But it was a PAIN in the Crystal version of the game since your pokeGear space was limited, because some trainers offered wonderful benefits (there were four trainers who you could talk to that had evolution stones which were painfully rare in Gen II), decent leveled pokemon for rematches (considering the level curve, this was needed), or insights into rare pokemon. Decisions weren't easy.
Protect and Detect. While in metagame, they can be the line between win and loss, in normal play they're most of the time annoying. It wouldn't be as bad if not the fact some of Pokémon learn them naturally, meaning you're bound to see AI spamming Protect/Detect on average Trainers, which will do nothing on longer run unless it's a battle facility.
Baby Pokémon. Much ire could be directed at them, but the main issue with them involves breeding. Baby Pokémon cannot breed at all, not even with a Ditto. This requires evolving them in order to breed them. Some Pokémon can bypass this by not having the proper incense when breeding, * So if you put a Sudowoodo in the Day Care and it can breed, the resulting egg will yield a Sudowoodo. If the Sudowoodo parent is holding a Rock Incense, the resulting egg will yield a Bonsly instead. but some will hatch as babies anyway * Pichu, Cleffa, Igglybuff, Togepi, Tyrogue, Elekid, Magby, Smoochum, and Riolu, complicating the process. If you want to chain-breed, or breed for good IVs for the ones mentioned above, put on your patience hat. Most baby Pokémon evolve by happiness (see above), and a few evolve by level (Tyrogue at 20, Smoochum/Elekid/Magby at 30). So, you have to grind their levels or happiness just to get to the next step in the breeding process. Also, some Pokémon can only learn egg moves as a baby (Roserade can only learn Extrasensory if it hatched as a Budew; it will not learn it if hatched as a Roselia), complicating this further. At least wild baby Pokémon, in Generation VI, are guaranteed to have three IVs of 31.
Pokémon that require trading to evolve are obnoxious enough, but the ones that also require a specific item to be held while trading in order to evolve are even worse. The items they need to hold are either rarely held by wild Pokémon, found only by Pickup users near the level cap, or the item is only available once per game. Fortunately the one-of-a-kind items are purchasable in X and Y in the Battle Maison. In some games, the trade-with-item evolutions are rare wild encounters, which can also help somewhat for those who just want them for Pokédex completion.
Don't even bother trying to search on the GTS for these Pokémon. Out of a selection there will be one Pokémon at the most with the required item... and the offerer either wants a legendary for it or the evolved Pokémon you're trying to find. Every single time. Try to search for its evolved form and the results are the same but less in number. If you offer something and ask for the unevolved Pokémon, there's no guarantee it'll have the necessary item, even if you specifically request it holds the item. The Porygon line is the worst, as it needs to be traded while holding a specific item twice with different items each time to fully evolve!
Started or Originated in Gen III
The Pokéblock system in Generation III. It seemed like Contests in that it could be seen as a minor gimmick you can move on from and forget about. However, it's necessary to evolve the already elusive Feebas into Water-type powerhouse Milotic. Cue hours spent tending to Berries, making Pokéblocks and stuffing its ugly face with them until it reaches the right Beauty value. Don't forget that Pokéblocks take the place of bait in Hoenn's Safari Zone (as well as the fact that there's always a chance that a wild Pokémon won't like the Pokéblock thrown at it). Want that rare Phanpy to not run from you? Better make more Pokéblocks! GameFreak thankfully fixed their mistake with Feebas in HeartGold and SoulSilver. Massages from Daisy will raise a Pokémon's Beauty, and nature will not affect it. It is still a Guide Dang It moment, but hey, at least you don't have to find the right-natured Feebas, then be nearly perfect at blending rare berries, then PRAY that the Pokéblocks/Poffin are high enough quality to bring Feebas to a high enough Beauty. Fixed even further in Generation V. Feebas evolves if traded while holding a Prism Scale. The old method still exists, if anyone transfered a Feebas capable of evolution.
Speaking of Feebas, just finding one is a Scrappy Mechanic in and of itself! They appear only on Route 119 in six specific squares chosen at random (and Route 119 is particularly large). Worse, even on the right square you only catch a Feebas 50% of the time per fishing attempt, making it even harder to tell which squares are the right one. It's even more annoying in Diamond/Pearl/Platinum. In those games, Feebas only appear in four random squares in the lake in the bottom of Mt. Coronet, and they only have a 35% chance of appearing per fishing attempt. Worst of all, unlike in Generation III, the specific squares that Feebas appear change daily! It's enough to make you want to tear your hair out. It's thankfully far less of an issue in Black/White, as they're fairly easy to find on Route 1 in Unova.
The third generation introduced the split between the Regional Pokédex and National Pokédex. Basically, rather than allowing old and new Pokémon to be found wherever you go, a la Generation II, now you can only catch the newest ones (with a few old standards like the oh-so belovedZubat) until you unlock the National Dex which will finally allow you to encounter older Pokémon. The catch? The National Dex can't be obtained until you've pretty much finished the main game. True, you can trade regardless of what Pokédex you have, but it does seem like the developers were a little too keen to ensure you used the new Pokémon.
In the Sinnoh-based games, you can't even access the National Dex until after you've seen every Pokémon in the Regional Dex. If you're not careful, you might miss some, but it's generally easy to do. The problem is that many don't appear until late in the main game.
Pokemon Black And White take this to its logical conclusion: the Regional Dex for Unova doesn't have any of the prior 493 Pokémon. This is a bit of a mixed blessing: no more Goddamned Zubat but no more old favorites like Eevee, Skarmory, Blissey, or Pikachu. That's right, even the Series Mascot is getting the boot until you get the National Dex.
The second Unova regional Pokédex seen in Pokémon Black 2 and White 2 has 300 Pokémon, with nearly half of them returning from other regions. This includes Zubat, though. (Thankfully, they're much less common.)
This problem arises yet again in Black 2 and White 2 for completing the New Unova Dex. Unlike the previous game where only 1 Pokémon cannot be seen without trading (Rufflet or Vullaby, depending on the version), in the sequel game there are plenty more of which you won't see. Normally this would you mean you can "see" the missing Pokémon via breeding (for some odd reason some of the wild Pokémon are already evolved with no trace of the starting form) or evolving. However, there are Pokémon who you won't be able to see at all. Rufflet or Vullaby is among them. The starting and final forms of the starter Pokémon you didn't pick won't also pop out. Do note that you won't be able to seek Pokémon you haven't seen in your Dex yet, you cannot ask specifically for those on the GTS either, and that you won't be able to visit the Nature Preserve without a complete Unova Dex.
The Kalos Dex in XY is so large it had to be split into three. Fortunately, the National Dex is unlocked by beating the Elite Four, and you only have to see every Pokémon in the three regional dexes to unlock the Oval Charm. Unfortunately for completionists, Pokémon transferred up from older games only count for a lesser tier of completion; you'll have to breed new ones in X or Y for it to fully count (and you're out of luck with legendaries).
Fire Red and Leaf Green's evolutionary system is this to many people - before you obtain the National Dex, if you have a Pokémon that attempts to evolve into a Pokemon introduced after Generation I (eg Golbat attempting to evolve into Crobat), it will automatically cancel the evolution. Eevee is also incapable of evolving into Espeon or Umbreon due to the fact that the games have no time system, meaning it can only evolve through RSE or XD. Ironically in the latter, you're given the opportunity to receive an item that allows you to evolve Eevee into its Generation II evolutions - a Sun Shard for Espeon or a Moon Shard for Umbreon. They sure sound like the kind of items you wish were in FRLG, and what makes this worse is that the GameCube, and thus XD already have an internal clock system anyway.
Heart Gold and Soul Silver are also guilty of a similar situation, but to a lesser extent. They may have updated the Johto Pokédex to include the evolutions of several Pokémon who evolve while knowing certain moves, but didn't Retcon any areas to allow Magneton, Eevee and Nosepass to evolve into Magnezone, Leafeon/Glaceon or Probopass respectively, despite the range of possible areas (Near the Power Plant's generator, Ilex Forest/Viridian Forest or the Ice Path).
Started or Originated in Gen IV
The Global Trade System (GTS) in the Generation IV games was an excellent concept, especially for people who've missed event-only Pokémon, but its terrible execution prevents it from being useful. Some of its flaws, in no particular order:
You can only search for Pokémon you've seen in-game. This makes it nearly useless for completing the National Dex since there are many species which you will never encounter unless you follow obscure steps to make it possible for them to appear, and many others that you simply won't ever see unless you get one somehow. It doesn't help that battling other players and playing the special battle formats don't fill out the "seen" entries.
Fixed in Generation V. In Pokemon Black And White, over 100 Pokémon are unobtainable via normal gameplay, but most of them (such as the Eeveelutions, Garchomp and Scyther) are used by NPC trainers during the postgame - if you battle the NPC trainers, you record the unobtainable mons as "seen", allowing you to trade for them over the GTS. This was probably done to make the GTS a bit more of a help in completing the National Dex.
Even better in Generation VI, as while you still can't outright search for Pokémon you haven't "seen", there is an option called "What Pokémon?", allowing you to type in the name of any Pokémon to search for it.
Search results are heavily limited (a maximum of 7 results per search) and they restrict it even further if you haven't been using the system much. You start with 3 search results and get upgraded to 5 and 7 by having made trades recently. While this was presumably done as a way to encourage people to be active in trades, it comes across as punishing players for not being able to use the system well by making it harder to use. The only way to work around this and find more search results is to restrict your searches - say, look for a level 9 or under male, then a level 9 or under female, then a level 10+ male, then a level 10+ female, etc. (Luckily, this mechanic has been removed in Gen. V, letting you get up to 7 search results every time, regardless of how much you use the system.) And you will need to refine your search results, because...
The system has no way of filtering or enforcing a concept of reasonable trades. It is largely clogged up by trade offers that are absolutely ridiculous (Offering a level 1 Bidoof and asking for a level 100 Deoxys) or even impossible (I'd like a level 20 Dragonite, please).
The impossible ones are often done on purpose, with people exploiting a Good Bad Bug that lets you clone. It can really backfire if someone actually trades them a hacked Pokémon in the process, though. Others store mons on the GTS when their PC boxes are nearly full.
The above has gotten even worse in Gen. V, as people seem to actually be looking for hacked Pokémon this time. You can't even search for a Pansear without seeing people asking for Lv. 9 and under Zekrom and the like. And if you deposit a Pokémon yourself, expect hours to go by with no results, due to the limited search results... all clogged by the aforementioned Lv. 9 and under Zekrom requests. The saddest part is that you can't even submit such a Pokémon, as the game detects illegitimate Pokémon and refuses to let you trade them. Why wouldn't Game Freak enforce such detection also for these requests is anyone's guess.
GTS trades won't allow you to filter or even see the ability or the nature of a Pokémon on display, leaving the thing for Pokédex purposes only, as bad as it is for that purpose already.
GTS Negotiations is a slightly less awful alternative. Instead of leaving a Pokémon and waiting days for a trade, you can hook up instantly with that one guy who decided to fire up the feature at the exact same time as you! And you can propose not one, but a whole three of Pokémon for your partner to pick one while you pick one of his three proposed! You can exchange for Pokémon you have not seen yetnote yet you cannot specifically ask for them because their name won't show up in line-building until you register them! What is best, you can see Abilities and Naturesnote assuming he didn't disconnect during the Mon picking phase where these cannot be seen because you didn't put a Zekrom up for grabs! Too bad that Game Freak, understandably, was afraid kids would spread swear words through their PEGI+8 game's multiplayer features, reducing your communication possibilities to four bland, ambiguous emoticons (:D, D:, <3 and !) and a single sentence built out of premade lines with a handful of words for you to fill in. At least you can ask for a specific mon or two in that line, but no one seems to read it and/or have what you are asking for.
Sometimes in Gen. V, you can't even CONNECT to the darned GTS because it's so flooded with people trading blasted Magnemite. (see the Join Avenue area below) You'd think that the powers-that-be would update the servers used for the GTS sometime to handle higher loads once they realized what people were doing.
Generation VI fixes a lot of the issues with the GTS. You can search for any Pokémon if you know its name, even if you never saw it, you get more than seven results, and you can even filter the results not to show people requesting (most) legendaries or Pokémon you don't have in your PC. While the "impossible trades" thing is still an issue and the results are flooded with requests for legendaries even with the "special Pokémon" filter active (the filter only accounts for Pokémon that are not tournament legal, rather than including all legendaries, so you still get people looking for Entei and Latias), it's a step up.
Vespiquen. It evolves from Combee at Level 21, but only if it's female. First, wait no less than six hours due to the Honey Tree mechanic, then you have roughly a 20% chance of finding a Combee AND a 12.5% of it being female. Didn't find a Combee? Too bad, the species is decided when you slather the tree, so you'll have to try again and wait another six hours. Gender can be decided, though. So you can save beforehand and keep restarting until you get a female. Or just get one of either gender and breed with a Ditto until you get a female.
The honey tree mechanism itself could also be considered a Scrappy Mechanic. There are 21 trees throughout the game in Diamond, Pearl, and Platinum which one can slather with honey, and between six and 24 hours later could come back to find one of a number of Pokémon there. The species is set once you slather the tree, so there's no real way to manipulate what Pokémon appears (if you decide to not save and turn it off if it's the wrong species, then you've just wasted the last 6 through 24 game hours). It's also incredibly likely that a player will forget to check a tree after slathering it, and after 24 hours the tree resets and to get a Pokémon from it you have to slather it again. Oh, and a number of Pokémon can only be obtained from these trees (without trading). One of them is the infuriating Munchlax, which only appears in four trees out of twenty-one, and the game gives you no indication as to which four trees these are. And to make it worse, it only has a one percent chance of appearing on those four trees. It could potentially take months to find one.
At least you can now find a wild Combee in Gen V. Much easier to get that elusive female. And Munchlax? Wait 'til summer in Unova, get the right Pokemon and trade the NPC for it.
Catching Beldum in Diamond/Pearl/Platinum, which has the same catch rate as an average legendary, is around Level 52, shows up only on a certain day (it IS a swarm Pokémon after all) and the only move it knows is Take Down. Metang and Metagross can be found in the wild in Generation V, and while they lack Take Down and can appear on any day, they still have the lowest possible catch rate.
Serene Grace Flinch makes many competitive battlers' blood boil. There are three mons (Jirachi, Togekiss, and Shaymin-S) with access to a move that has a 30% chance of causing the opponent to "flinch", a.k.a. miss their action for that turn, and the ability Serene Grace, which doubles the chance of any added effects taking place - to 60% in this case. Togekiss frequently combines this with paralysis, which adds an additional 25% chance of skipping a turn. Jirachi frequently combines this with a Choice Scarf, making outspeeding it nigh-impossible outside of mons with normally overkill Speed such as Speed Forme Deoxys. And Shaymin-S has access to the move Seed Flare, which has a whopping 80% chance with Serene Grace factored in to double the damage of its flinching move. Any of these mons can easily flinch an opponent over and over and over until even should-be counters are dead. When Shaymin-S was nominated for banning by Smogon...well, let's just quote the overseeing moderator on the results:
"That's right folks, we just made history. Smogon just had its first unanimous vote ever! I would like to take this time to thank Shaymin-S for being so annoying that literally every voter wanted to ban its ass."
Started or Originated in Gen V
The Pokémon Dream World. It was originally for getting Pokémon with new or different abilities, but everything about it was a pain:
It's the only place to grow berries in the 5th Generation games; berries cannot be transferred from a Generation IV game (so no internet connection means no berries), and you started off with only 6 berry plots and a maximum of 15.
A mechanic punished you for inactivity on the Dream World. If you go more than 100 days without using the Dream World, all of your berries, save for one of each kind, were taken away and converted into Dream Points.
It crashed all the time. That's annoying enough in and of itself, but it also means you might not have been able to water your berries, so you might have lost them through no fault of your own.
A lot of the mons simply weren't available on the Dream World, so their new abilities couldn't be obtained legally. Many aren't available as females, so you can't breed their good abilities onto Pokémon with Egg Moves or better IVs/natures.
The sheer amount of time to "tuck" a Pokémon in: it could take upwards of five minutes to send one to the Dream World from the cartridge and about that much time to retrieve it from the Dream World, and you had to do this every time you wanted to get a single Pokémon from the Island of Dreams.
Also, visiting the Island of Dreams threw you in a random location instead of choosing which part of the Island you wanted to visit. Stack that on top of Pokémon ceasing to approach you for the rest of the day after you visited the island enough times, and it could get pretty aggravating, especially if there was a certain Pokémon in a certain location you were after.
Sending in certain types would increase the chances of visiting a specific location- Normal-types tended to visit Dream Park, Water-types tended to visit Sparkling Sea, and Dark, Ghost, and Psychic-types tended to visit the Spooky Manor, and so on, but good luck trying to get to Windswept Sky reliably- you were less likely to visit that place because all but one Flying-type is dual-typed.
Earning enough Dream Points to unlock berry plots and Island of Dreams locations was also a pain, since the only way to increase them is to water other people's berries (you could only water 30 berries per session), complete minigames, log on to the Global Link once a day, and gain a Dream Pal. Good chances are your only option is to grind up minigames, which tended to be tedious (I'm looking at you, Blow Out the Candles) and only gave 20 Dream Points apiece.
Finally, you could only choose one Pokémon to take with you. No matter if you befriended tons of potentially useful mons, even a rare female Fossil Pokémon- nope, it's only one you get to take per visit. And once you've taken that one, there was no more going to the Island of Dreams.
There was no way to add any of your real-life friends as dream pals. Instead, you had to rely on an ever-so-slight chance that you'd encounter their dream home when you decided to venture out and visit other people's homes. Otherwise, your "dream pal" list was gonna be full of total strangers that you can't communicate with beyond vague, fill-in-the-blank phrases.
Many Hidden Abilities are only available on Pokémon obtained from the Dream World. Need a Corphish with Adaptability, Lileep with Storm Drain, Carvanha with Speed Boost? Hope you got one before it shut down, or you'll have to find somebody else who did.
As of December 10, 2013, the Pokémon Dream World for Pokemon Black/2 & White/2 has been shut down, preventing players from using the original Dream World and collecting the Pokémon with available hidden abilities, along with growing and collecting berries and changing C-Gear and Pokédex Skins in their games. This is to replace it with the new one for X & Y while giving players compensation with Miles and medals based on their prior progress.
Black City and White Forest, in the original games. Both are cool places, but to keep them at their best, the player must regularly use Entralink and the C-Gear. Otherwise, the player must fire the game up and talk to all available residing people almost every day to keep them from leaving. Thus, these locations are fairly useless to anyone without a lot of local friends who play a lot of Pokémon. Adding to that, they discourage casual playing. For Black City or White Forest to be anything resembling worthwhile, you have to get there (which requires beating the entire story) in LESS THAN A WEEK. For some players, this seems to be a complete impossibility. The sequels opted to ditch the Socialization Bonus aspect and have both areas contain a unique Bonus Dungeon instead.
The Join Avenue is one of the greatest Game Breakers of the franchise. It's therefore understandably tedious to grind up to Game Breaking levels, but just making some use of it takes a good deal of time. You'll only get a set number of daily visitors based on your Avenue Rank. You'll have to decide between either building few stores to rack up points early (which level up the Avenue and bring in more daily visitors), or building a variety of stores to ensure you will not have any visitors who dislike everything you have (even with their "I want to go there!" speeches). Another source of visitors are other players whose IDs you have registered through the C-Gear's features (unlikely except if you live in Japan) and online battling and trading. To give you an idea of the impact the Join Avenue had on the GTS, Black 2 and White 2 gave birth to the "Magnemite Stock Market". Magnemite are available early on, easy to catch, and are drawn to you thanks to their Magnet Pull ability. They became the premier ID exchanging vessel and the most demanded, the most offered and the most exchanged Pokémon in the GTS, and remained that way for the generation's lifespan.
In Pokémon Black 2 and White 2, Pokémon Breeders will always confront you for battle when you pass by their line of sight, even if you've already defeated them and regardless of your level. This is reset whenever you leave the route and come back. You can avoid theOm by hugging the edge of the path, because unlike most trainer classes Breeders have a limited line of sight, but this is not something you will think about when you're in a hurry to get somewhere, for example, leading to a completely pointless battle.
With a little practice, you can easily dodge them by passing by at the moment their backs are turned, or simply taking the long way around. This can still be annoying when your monsters are low on health and "the long way around" happens to be a big patch of grass/sand, though.
The fact that male and genderless Pokemon can't pass on abilities, especially when figuring in Dream World abilities. Want a male-only species like Sawk or Tauros with its DW ability but can't connect to the Dream World for some reason? Sorry, you're out of luck unless you can get someone to trade you one. Ditto with the starters - when released from the DW, they're always male only. At least with females, you can trade or have one bred for you with its DW ability. As of Generation VI, this is no longer an issue for male Pokémon, albeit only while breeding with Ditto.
Hidden Hollows/Grottoes in Pokémon Black 2 and White 2. They're great for getting some Dream World ability Pokémon in the game itself, but over half the time, they have items or mulch in them. And the mulch is just Vendor Trash since berries only grow in the Dream World, and unless you're broke, mostly useless. And then they start repeating Pokemon... one or two extra are okay for trading, but then it's like "enough already!"
It's worse than that. They are far out in areas and require some distance to reach. And, like mulch, you're more likely to find worthless Repels and regular Potions. As for Pokémon, you have to engage in battle and defeat/flee from them so the grotto can regenerate something else... which has a 5% chance of occurring every 250 or so steps. Yeah, even Pokémon that are common or uncommon in encounter rates may be more likely to be Metal Slime by the Grotto's standards considering the effort and mess one has to go through.
The final games of Gen V finally bring a hard mode to Pokémon (referred to in-game as "Challenge Mode"), meaning that more skilled players no longer must rely on Self Imposed Challenges to keep their single-player experience fresh. Unfortunately Challenge Mode is crippled by strange, seemingly arbitrary restrictions. Only Black 2 players can unlock it, while White 2 players instead get a pointless Easy Mode. However, Challenge Mode is only obtained after you have already beat the Pokémon League, mitigating much of the appeal. You can't enable Challenge Mode and then restart the game without losing it. In order to play the entirety of Black / White 2 with Challenge Mode, which is what most players looking for a difficulty boost would obviously want, you must have someone gift it to you. Except it can't be via wireless- only the terrible IR port, used through the top of the cartridge, works. In conclusion, to play Pokémon with the sort of difficulty option 90% of games let you select from the start, you must either A: own two DS's and two Black / White 2 games, one of them being a copy of Black 2 you already beat, or B: have a friend you can meet in person who owns Black 2 and has cleared the Pokémon League. It may not be an insurmountable obstacle if you live in Tokyo, but it's a series of completely unjustifiable restrictions for the majority of older Pokémon fans, who are the sort of people who would want the option in the first place. All these restrictions apply to Easy Mode too (substituting 'White 2' for 'Black 2' where appropriate), which means anyone actually needing that lenience is unable to obtain it.
The fact that every time you switch systems, the Dream World and Join Avenue take mostly a whole day (24 hours for the Dream World, and later reduced to 20) to reset, and all your friend codes get wiped out if you try to connect to the GTS on different systems. Some folks still switch between a 3DS and a DSi or classic DS for lack of a 3DS compatible Action Replay, and it's aggravating.
Started or Originated in Gen VI
Pokémon-Amie has a minigame where you make facial expressions as an on-screen indicator shows. Simply starting the minigame requires lots of background light, the 3DS facing you in such a way a face indicator shows up, and tilting your head enough that it starts. The biggest problem is that the game barely recognizes the expressions. You'll be grinning like an idiot and tilting your head, yet the game won't recognize you and your Pokémon will be disappointed. If it tries to ask for a smile, you'd be lucky if it even recognizes the "small smile." At least you don't have to use this minigame at all if you want to max your Pokémon's Affection.
While introduced in Generation IV, the censorship on nicknames became far more noticeable this gen. Before, the GTS would refuse to allow Pokémon with certain strings of characters in their names (which would often fall victim to the Scunthorpe Problem). Now, you can't even name the Pokémon with names with those strings in the first place, even if you never intended to trade them at all! The banned strings include banned words in other languages entirely, even if they're perfectly harmless in your native language, and can be really obvious when you try to name a Pokémon "Violet" or "Spike" — not only perfectly valid names, but there is a prominent character in the game named "Viola", which is also banned! The filter frequently fails to catch legitimate swears... If you transferred a Pokémon from a previous generation with a nickname the system deems inappropriate, it'll simply wipe its name when it comes over. So if you wanted to keep the nickname, and its nickname was not explicit yet blocked by the system, you'd have to figure out what nickname was closest to the original that is not blocked on X and Y and then go back to the previous game and rename it there. Infuriatingly, several of these blacklisted words under certain circumstances such as adding another character to either end, render them able to pass through the filter while other blacklisted words are left without the distinction.
Poké Transporter. If you want to transfer over a lot of Pokémon from your Gen. V games over to X and Y, you're in for a long process. First, you must make sure all of the Pokémon you want to transfer over are in the first box of your Gen. V game. Then you must boot up the Transporter and transfer them over. Then, you must go to the Bank and transfer the Pokémon to either your X/Y PC boxes or the Pokémon Bank boxes. Then, if you want to transfer more Pokemon over, you'll have to go back to your Gen. 5 games and move them all to the first box again. It's much faster and less tedious than the Pal Park and Poké Transfer, but it still gets unnecessarily tedious after a while, especially with the constant connecting/disconnecting of the Bank and the Transporter.
To make things even worse, the Pokébank app is incompatible with Gen. V games and will only run when a Gen. VI game is inserted into the 3DS. Since you need your Gen. V game in to take Pokémon off of it, and you can only transfer one box before the system makes you start up Pokébank and empty the transfer box, this means that you must continuously switch the game cartridges back and forth. Not only is this a huge annoyance, but the constant and repeated use has actually caused damage to the springs in some 3DSes, resulting in either a cartridge getting stuck or the system being unable to read them.
The Poké Transporter and Pokémon Bank's hack detection is (controversially) wonky. Sometimes it will let blatantly hacked Pokémon like shiny legendaries with perfect stats through, or Pokémon with unreleased Hidden Abilities (like Snivy with Contrary or Totodile with Sheer Force). Other times, it will refuse to let perfectly legal Pokémon through; event legendaries are frequent victims.
Horde battles have a rare chance of one or more Pokémon having their Hidden Abilities. Great! Is the Pokémon a species that doesn't appear in the Friend Safari? Is it an ability that requires you to scan each member with Role Play or Skill Swap? Get out the patience hat, because that's what you'll have to do to find one. Pokémon in hordes have their Hidden Ability at about a 5% chance. You'll have to go through a lot of them to find one, and if you do find the right Pokémon, you'll have to withstand all their attacks while trying to scan and trim the horde to the last one.
Serial code-based distributions are beginning to draw the ire of some fans. In lieu of a wireless distribution that is limited only by time, these things are limited in terms of quantity as well, and information on which locations are doing the distributions is often scarce. Many people who have gone to stores giving out these codes have complained that even though they are supposed to be handed out for free, employees often refuse to surrender the codes unless they purchase something else as well. Even after inputting the code, you need to connect to wi-fi in order to activate it, making the process quite redundant in some aspects.
Obtaining the Eon Ticket, required to access Latias/Latios (the one that doesn't appear in each version), in Omega Ruby and Alpha Sapphire, combines several Scrappy Mechanics from its page. It starts off with a serial code (see above) only available to certain players. Players must use StreetPass to obtain the Eon Ticket from other players once the code distribution runs out. In many places, StreetPass isn't feasible.
Wonder Trade. It's a blind trade, you offer something for trade and a random partner is found to trade with you. The trouble is, the feature gets flooded with Com Mons. People start using it as soon as they get the game, in hopes of getting good pokes. But all they have at that time are junk Pokemon from early in the game. And some are just lazy, wanting something for nothing. Either way, you'll get a lot of Scatterbugs, Fletchlings and starters, and only rarely will you get decent Pokemon.
Pokemon Stadium was programmed with an anti-cheating mechanic that wouldn't allow you to transfer any data from a Red/Blue/Yellow game save that was tampered with a cheating device like a Game Shark. Which was fine and all... except for the fact that it also refused transfers from saves which had encountered natural glitches, even something as basic as encountering a Missingno. And even worse was that some game paks still wouldn't transfer even if you deleted the save and avoided glitches.
Pokemon Stadium 2 had the Prime Cup which required the player to have six level 100 pokemon to compete in it. If Gen II was your starting game, then you had an absolutely miserable time raising a team to 100 because of the god awful low level curve in those games that made it tedious to train a team up for competition.
If you trade a mon from a Gen II game who knows moves that existed in Gen I, but could not learn naturally in Gen I, the same thing also happensnote Keep in mind the region lock only checks that a Gen I mon doesn't know a move that doesn't exist in Gen I, as long as the move exists in Gen I, it will let it be traded, even if that species couldn't learn that particular move in Red/Green/Blue/Yellow's time. This commonly happens among egg moves, an example being Bulbasaur, who cannot normally learn Light Screen in any way in R/G/B/Y, but can learn it as an egg move if bred with a Chikorita, Mareep, or either of their evolutions who know the move. Because Light Screen existed in Gen I, Bulbasaur can be traded to a Gen I game, but because Bulbasaur couldn't learn Light Screen then, Stadium reads the Bulbasaur as a hacked Pokémon.
Being a side game and all, it's understandable that Pokémon Mystery Dungeon would change the way a few of the moves work. Some changes, however, should not have been made. Spite removing all of a move's PP as opposed to only four and Knock-Off potentially rendering a held item permanently unusable, to name a few.
The Monster Houses from the Pokémon Mystery Dungeon games. Quite annoying when you spawn in one, or just enter one altogether.
Eugh, quite annoying? Try highly. Take Sky Tower in the first game. The selection of Pokémon in it include Aerodactyl with Pressure (lowers your PP quicker) and Agility (raises the speed of EVERY enemy Pokémon by 2), ghosts like Shuppet who can sneak through the walls and attack you while you can't attack them back and who have Curse which takes away a quarter of your health each turn, Shedinja who can only be brought down by certain types of moves (and can also sneak through walls), Koffing who can and will poison you, Lunatone who can send you to sleep rendering you helpless... Get all these lovely creatures in one room, multiply their numbers by 5, give them a fierce desire to murder you and that is what Monster Houses are all about. And what if you enter one so your teammates are unable to help you? They'll either stand idly by and watch you get slaughtered or prance off to find a way around to get to you and get knocked out themselves, which is usually what will happen unless you spawn in one.
Perish Song. The hit rate is fairly low, but when you've got a half dozen Politoed spamming it like there's no tomorrow, the law of averages is bound to catch up. Once you've been afflicted, you're boned unless you can reach the stairs in 3 moves or are packing a Heal Seed or two.
Explorers of Sky hit a few new lows with these things:
One type of trap surrounds you with enemies, and then gives all enemies on the same floor a status condition which drains all your Power Points of the move you used to KO it. The status condition is applied to every enemy that is on the floor at the time it is triggered, never wears off, can't be destroyed by anything, and the dungeons these appear in are ones which prevent you from bringing items in for refills (or allow limited items, which isn't quite as bad but still difficult). To add on to that, if you've already used any move while on the floor, even if you knock out the foe with the Grudge status completely with your normal attack, the last move you used loses all its PP. The only way you'll be safe is if the foe is knocked out by an effect that wouldn't give you any EXP afterwards (recoil, Pass Scarf, etc).
Another type of trap randomly chooses one of the possible types of traps, then applies the effects to your whole party whether or not anyone else stepped on it.
And the worst of all: The new Brutal Bonus Level keeps all traps invisible, whether you've stepped on them or not, and whether you are using any item that normally makes them visible. Okay, Luck-Based Mission, we get the freaking point already.
The Aegis Cave mission in Pokémon Mystery Dungeon certainly counts, mainly because it's the most frustratingly tedious mission in the entire game. And, yes, it is mandatory. Basically, all you do is try to solve three word puzzles by spelling out the words ICE, ROCK, and STEEL. To do this, you have to collect stones with the correct letters on them from the Unown (Trust me, you'll run into plenty of Unown). Unfortunately, the Unown that drops the letter you need must be randomly chosen for the list of available Mons, then it has to randomly spawn, then you have to find it, and then, after all that, it only drops the damn stone 1/4 of the time! Which basically means you'll be going through the same parts of the dungeon over and over and over again until you slowly lose your sanity trying to collect whichever stones you need so you can get out of the blasted cave. Oh, and if you want to go back to recruit the Golems for 100% completion, you have to do it all over again. And it gets worse if you can't recruit a certain Golem the first time, because then you'll have to do it again.
In Pokémon Mystery Dungeon: Gates to Infinity, several features from the main-series Gen V games are carried over. One of them is that TMs are infinitely reusable. However, you can't teach a Pokémon a TM unless they're in a dungeon and since they're no longer consumable, they're left in your inventory. This means that you have to take two items (the TM and a Deposit Orb, to send it back to storage) and go into a dungeon, just to teach somebody a new move.
The save system in Pokémon Colosseum, that forces you to reach a PC to save your progress, instead of saving anywhere like most of the other games (save the Mystery Dungeon games).