These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Pokémon Ruby and Sapphire
Anticlimax Boss: One of the more noted weakness of this set of games is that both the rival (Brendan/May, who doesn't fully evolve his/her starter and is the only one who can't be battled infinitely) and the Aqua/Magma Admins (who only use a mere three Pokémon, all of them being ones that every one of their grunts use) are really pathetic compared to the rivals and Admins in the rest of the series.
Wallace as the Champion in Emerald is thought of as being this due to falling to Poor, Predictable Rock unlike Steven, who uses a diverse typing of Pokémon. Steven does appear as a much harder Bonus Boss later, though.
Tate and Liza are fairly easy in Ruby and Sapphire, only having two Pokémon between them, both of which are easily taken down by Surf which is required to get to their Gym in the first place. In Emerald, they have four Pokémon.
Wattson and Flannery are fairly easy to take down, provided you have Pokémon types they're weak to.
Elite Four member Drake can be considered super-easy to defeat as long as you have ANY Pokémon with an Ice-type move, as four of his Pokémon have a quadruple weakness to the Ice type. And the one who isn't, Shelgon, is comparatively low-leveled, not fully evolved, and still possesses a weakness to the Ice type. In Emerald on the other hand, he uses Kingdra in place of one of his Flygon, you can't just one-shot his team with Ice types.
Critical Dissonance: Believe it or not, the original Ruby and Sapphire received very positive reviews just upon release. The fandom was much more polarized for many reasons, and still is to a great extent.
Demonic Spiders: Although not hard to run away from, Whismur can do a lot of damage with Uproar. If you're not careful, it can result in a couple Pokémon dy-fainting.
I think Trapinch counts. It usually has Sand Arena, which means you can't switch out or run. The Pokemon you open with is the Pokemon that lives or faints. If you're just trying to pass through the desert, and you weren't really thinking about your lead Pokemon, and you come across a Trapinch...
Draco in Leather Pants: Sure, Archie and Maxie were some of the least openly-evil villain bosses to begin with, but some fans go even further and remove any traces of responsibility for their crimes from them. And then there's their underlings, who get this treatment as well despite being Psycho Supporters or Jerkasses.
Flygon has a pretty big underground cult following for being one of the coolest Pokémon designs of the third generation and for its unique typing. Even after Garchomp was released with the same typing and arguably better stats overall, many players prefer the good old insect/dragon hybrid because its just way too damn cool.
Aggron is pretty popular, thanks to a certain poster. (See Memetic Badass below)
Absol got a lot of love for its cool design, though its veryAwesome, but Impractical nature (it was a Glass Cannon with a massive movepool that couldn't use most of it because of its horrible Special Attack, while its similarly bad Speed ensured that it would get killed before it could do much of anything) made it a competitive pariah until X and Y, when it Took a Level in Badass with a terrifyingMega Evolution that fixed all of its problems and instantly turned it into a team-wrecking threat.
All of the enemies in the desert in Route 111 can be this, especially when combined with the perpetual sandstorm in that area and the fact that all of them have accuracy-reducing moves.
Sandshrew have high Defense and an evasion boost in the sandstorm, they can increase both advantages, and they can poison your Pokémon. If you aren't fielding a Pokémon immune to the sandstorm damage, they can go from this trope to outright Demonic Spiders after a Sand Attack or two.
Baltoy frequently Selfdestruct as the first move in combat, and if that fails, they may attempt to confuse your Pokémon.
Cacnea have the same evasion boost as Sandshrew in a sandstorm (as well as Sand Attack) and can pile Leech Seed on that.
Trapinch are the least offensive, but they can become this with their Arena Trap Ability if you're trying to flee the area and limp back to a place to heal.
And of course, Zubat/Golbat and Tentacool/Tentacruel return to fulfill their role as Goddamn Bats for caves and for surfing. Wingull and Pelipper make their debut as the worst of both worlds — speedy confusion-spammers on the sea — in a game that involves a lot of surfing.
The Berserk Gene item from Generation 2 was often considered bottom tier due to its side effect of causing confusion along with the Attack boost it gives. It would appear it would have some use in Pokemon with the ability Own Tempo, but 1. No pokemon that had the ability had a Attack stat that could benefit from the boost until Lickilicky and Purugly the next Generation and 2. Berserk Gene is no longer an existing item this game onwards.
Chimecho, found only in one area (Mt. Pyre) with a measly 2% encounter rate. Close to completely useless in battle.
Luvdisc, despite not being that rare, it's still counts because it appears at endgame. It's by far the worst Water Pokemon of the game, with terrible stats except speed. If this doesn't convince you, Smogon will
Skitty as well, thanks to it also having a low encounter rate and a mediocre learned movelist.
Nosepass, despite its humorous appearance. You just have to get lucky in finding one by smashing rocks in Dewford Cave, and it has rather poor Attack, more than likely making you think, "THIS is the Pokemon I had difficulty with in Rustboro?" Luckily, Gen IV was kinder to it by giving it an evolution in Probopass.
Ironically, the poster sings Aggron's praises for having moves it doesn't get until Generation IV.
Now there's an updated version◊ that also includes its Generation V capabilities.
Steven Stone, as the Final Boss, naturally fell into this; when Emerald came out and he was replaced by Wallace, Steven was generally found to be the more difficult of the two—thanks mainly to having a more diverse team—and this was compounded.
The one thing fans seem to remember to blame Game Freak for rather than Nintendo in the Pokémon games is the inability to transfer Pokémon from the first two generations' games to Ruby and Sapphire onward. However, this is - coincidentally enough - the one complaint that the company had no control over - the Game Boy Advance wouldn't allow interaction with the Game Boy and Game Boy Color games at all, even if they wanted to make it possible (which it probably would have been considering every other generation at least allows transfers from the old games to the new ones).
On the other hand, many people still don't realize eight years later that Nintendo is only the publisher and most gameplay issues, with the exception of "cutting off ties to previous generations," were actually due to Game Freak.
Well, Scrappy might be too strong of a word here, but Steven is considerably more popular as the Champion than Wallace.
Some prefer Steven to Wallace because Steven uses the Steel type but doesn't exclusively use Steel-type Pokémon due to the lack of Steel-types in the Pokédex, so he's a bit more of a Worthy Opponent than Wallace; who uses Water-types and is quite easy to beat. Some also prefer Wallace just because he helps Sceptile catch up...and the Water-type actually is rather powerful due to the "one type uses one stat" mechanic.
Also, after crossing the sea, fighting Team Aqua and the Sootopolis Gym, most people are sick of Water-types by this point.
The fishing mechanic as a whole was much more needlessly complicated than in the other generations. Previously and after, you would cast your line and wait a few seconds and either get a bite or don't. In this generation, there's a needlessly long series of button pushes that literally amounts to "Oh a bite! Oh a bite! Oh a bite! Oh a bite! Oh a bite! Oh a bite! Oh a bite! Oh a bite!"
Power Up Let Down: The Old Rod makes you go through this timing check only once per attempt. The Good Rod increases this to a max of three checks, and the Super Rod takes it all the way to a max of six checks. Have fun fishing with the Super Rod for that 15% chance of a Horsea! (Also fitting this trope, there are several routes where using the Super Rod reduces the types of Pokémon you can catch compared to the Good Rod.)
Berry farming could be aggravating, since it lacked any means of finding where you planted your berries. Certain Berries (mostly the rare ones) also required that you must water the Berry plant during each stage of growth (not multiple watering during one specific growth stage); otherwise, your Berry yield when you harvest the plant will be exactly what you started with: one Berry.
Puzzles involving steering the difficult-to-control Mach Bike.
The Bicycle concept in itself could be considered as well - switching Bikes requires the player to travel to Rydel's Cycles in Mauville City each time the player wishes to switch, as he/she is only allowed to take one kind of Bike (Mach Bike or Acro Bike) out at a time. Several puzzles also require a specific kind of Bike - the Mach Bike is used to navigate across muddy slopes and cracked tiles, while the Acro Bike is needed to traverse distinctive white rails and rocky platforms. Hoenn's Safari Zone is probably one of the best examples - one area requires the Mach Bike, while another requires the Acro Bike, meaning that the player can only visit one of them during a Safari Zone session.
That One Sidequest: Finding Feebas and evolving it into Milotic. You can read the full summary here, but in short, it involves hours and hours of systematic searching, endless fishing, finding/breeding a Feebas with the right nature once you've found a Feebas tile, and lots of Berry farming and Pokéblock making. At least it's easier than in Generation IV where the Feebas tiles get scrambled every day rather than by something reasonably under your control.
As of the fifth generation, finding Feebas is all but hardly a chore anymore as both it and even Milotic are available in the wild and far easier to find than before. With the release of a new evolution item, evolving Feebas is nothing short of easy now.
Obtaining a Lucky Egg in this generation. It's a hold item that boosts EXP gained by 50%, making leveling much easier. However, it's only held by wild Chansey. While you could use Thief to steal the item in other generations, In this generation Chansey only appears in the FR/LG Safari Zone, meaning that you have to actually catch the Chansey. They're rare, hard to catch, quick to flee, and only have a 5% chance of actually holding the Lucky Egg, making it nothing but a Luck-Based Mission. Most players didn't even bother.
They Changed It, Now It Sucks: When originally released, there was no hint of a Generation Iremake, meaning that around 184 Pokémon were completely absent from the games. The only hint that they would return was their isolated data, which usually indicates event Pokémon (a very beloved game mechanic). That, combined with a number of expies for the missing Pokémon, replacements for Team Rocket, no way to return to Kanto or Johto, minimal time-based events, and an overall similar structure to Generation I led many a fan to think the release of Ruby/Sapphire was a franchise reboot, and said fans were not happy.
Tough Act to Follow: Ruby and Sapphire had the dubious honor of following up on Gold and Silver. Gold and Silver were highly regarded as an Even Better Sequel, giving players more Pokemon, a longer game, and introducing a number of new mechanics to the series like Friendly Evolution, Night/Day cycles, and breeding. Pokemon Ruby and Sapphire in comparison got rid of the Night/Day Cycle, was a shorter game, and introduced a slew of Scrappy Mechanics.
Vindicated by History: On the other hand, most fans these days appreciate the games and Game Freak for understandably changing the often slapdash code of the previous generations into something more managable, while introducing new mechanics that improved battles. Note however that this is "appreciation" rather than "love"; Hoenn is still derided for being poorly designed.