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.
What if the Waterwraith is just a lonely woobie who wants to play?
Olimar is frequently told off by the ship for not giving Louie proper instructions on how to navigate the planet. Disregarding the fact that it's used as a method to explain controls to the player, one can only wonder if Olimar, who is otherwise so on top of things, privately believes that Louie will...slow him down. Do the math.
Was Louie accidentally left behind on the Pikmin planet, or did he intentionally choose to stay?
Did the Plasm Wraith capture Olimar For the Evulz or was it legitimately caring for him and was just overprotective?
Let's review the Raging Long Legs. On one hand, it has the most HP of any boss in the game. On the other hand it is horribly slow, and unlike its "lesser" version, the Beady Long Legs, it can be attacked at any time due to its massive size, which also makes it nearly impossible to miss. At worst, you may lose Pikmin if you don't clear out during one of its retaliatory rampages, which are very telegraphed and easy to get away from. Now consider that this is the second to last boss in the game, and boss of what is probably the hardest dungeon.
The Waterwraith battle may also count. This thing has been following you through the entire dungeon, but once you've got a few purples, it's basically powerless to harm you. The second phase of the fight is actually just a big joke...
The Scornet Maestro in the third game. Although it commands a horde of bees, if you have a decent enough squad of Winged Pikmin, some consider the battle easier than fighting some of the normal enemies in game. It can't attack by itself, you can chip down it's Scornet squad before it can make an attack making them easily dodgeable, and even if it does capture some Pikmin, it gives you way more time to rescue them than you really need. On top of that, the Maestro suffers from the same problem the Raging Bloyster did, in that it'll only ever go after the active captain regardless if they have any Pikmin with them, meaning you can have a captain with your Pikmin sitting idly behind it, and have another act as a meat shield to devert it's attacks. Unlike the Raging Bloyster however, it won't turn around while attack even if you switch captains, allowing you to get even more free hits on the guy. There's a reason more people have higher time attack scores against it than any of the other bosses in the rankings...
The Waterwraith being an anticlimax after horrifyingly stalking you throughout the dungeon makes it one of the best bosses in Pikmin 2 to beat down.
In Pikmin 3, despite being That One Boss, the Mireclops is considered this by some for several reasons: It's possibly the largest creature in the series, it's a very challenging fight, and it has a cool, yet strange, design.
Breather Boss: The Giant Breadbug, as to be expected from a boss that doesn't even act hostile toward you. It doesn't even get the standard boss theme, instead getting a more laid-back, goofy-sounding tuba theme.
Should be noted that, though a Vocal Minority, there are also a few people who felt Pikmin 3 focused a bit too much on the elements of Pikmin 1 instead of 2.
Demonic Spiders: Spotty Bulbears, especially in the second one. They're hard enough to kill in the first game without losing a sizable chunk of your force, but in the second game they come back to life if you don't harvest their remains quickly enough. Also, they DON'T SLEEP in the second game; instead, they're already awake and alert, patrolling around the area, often with Dwarf Spotty Bulbears following it.
Epileptic Trees: There are plenty of theories surrounding the nature of and possible connection between Goolix, the Waterwraith, and the Plasm Wraith. The other major theories surround the relation between Louie and the Titan Dweevil.
Even Better Sequel: The general consensus about Pikmin 3 is that it takes everything that made the first game great and improves on it times eleven. The bosses are more cinematic and engaging, the overworlds are much bigger, Pikmin orginzation is much simpler, and the time limit is much more linear without losing the sense of urgency of the original. Some are even going as far to say Pikmin 3 is the first "true" sequel and that Pikmin 2 looks more like a Mission Pack Sequel in comparison.
Evil Is Cool: Some of the monsters, mainly the bosses, can be this.
A lot of people tend to refer to Rock Pikmin as simply 'Rockmin'. May or may not have to do with a certain blue robot's Japanese name. People also tend to call Winged Pikmin 'Pink Pikmin' simply out of tradition.
There's also the 'Koppai Crew' for Alph, Brittany, and Charlie.
In Pikmin 2, Purple Pikmin themselves are considered this to some, although their slow speed and lack of immunities, combined with them having no Onion and thus can only be made through the rare Candypop Buds underground firmly lands them in the Too Awesome to Use club for others. (Especially since you need to make 100 of these guys in the late game to get a certain treasure.)
Winged Pikmin, despite being weaker than other Pikmin and lacking immunities, can still completely bypass a lot of the puzzles in Pikmin 3 and get fruit much earlier than you should due to their ability to fly. A few examples are the second half of the scale puzzle in the Garden of Hope, in which normally you're suppose to use all three captains in a complicated counter balance puzzle to get the fruit at the very end. However, locking onto the fruit and using the charge command makes the Winged Pikmin fly up to it and take it back to the ship with zero effort. There's also the multiple 'slope bags' used to make shortcuts to areas. By using the dodge roll whistle, you can cause the Winged Pikmin to fly up into the air, have them charge the bag, and push it down with out having to reach it the conventional way. Then there's the part where Louie steals your juice and runs off. Using Winged Pikmin, you can skip 75% of the puzzles that require Blue Pikmin. It has to be seen to be believed. (Starts at around 1:02:35) On top of that, despite being weaker than the other Pikmin, their constant flight allows them to charge the weak spots of bosses other Pikmin normally can't, and using spicy spray to negate their low attack power can make some bosses (such as the Mireclops) much easier.
Hell Is That Noise: *WEEEESHHHH* *CRASH* *WEEEESHHHH* *CRASH* *OOOOOOWARRRRRRRRR!!!* followed by the sounds of illegible mumbling and the sounds of Pikmin being helplessly squished.
In Pikmin 2, we have the Antenna Beatle. Although it can't hurt your Pikmin on its own, it can use its wings to produce a very creepy tune, which interferes with the Treasure Gauge and attracts Pikmin, much as the Captains' whistles do. This can lead the Pikmin away from you and into another hazard close by.
The sounds the Plasm Wraith makes as it chases you in its transparent form in Pikmin 3. The background music doesn't help, either.
There's also how you can have Pikmin carry the playable characters back to base in the first two games. Louie must be carried back twice in the third game, and the entire final area is saving Olimar from the Plasm Wraith.
Pretty much all of the bosses and mini-bosses, but special mention goes to the Smoky Progg, the Waterwraith, and the Plasm WraithEldritch Abomination creatures from the first, second, and third game respectively.
Mushroom Pikmin. They don't hum or grunt as they chase you down. They just laugh.
On a no-Pikmin-death run, the Segmented Crawbster probably takes the cake.
Empress Bulblax, the second and third times around. Her continuously-spawning babies kill Pikmin instantly, and it's easy to let one slip your sights and have a feast without you realizing until it's too late.
Man-At-Legs. He can kill a WHOLE GROUP of 100 Pikmin if you're careless enough! Especially in the Hole of Heroes, where you have to fight it in a pool of water, meaning only blue Pikmin (and Bulbmin) can fight it. It's possible to lure it to where non-blues can get it, but it's difficult to the point of probably not being worth it.
Waterwraith on levels 1-4 of the Submerged Castle. He's easy enough prepared, but when you don't expect it and are not prepared, you can be devastated quickly, because it's merciless.
The Smokey Progg is technically more of a Bonus Boss, but it's guaranteed to catch players off guard the first time it appears, right before mercilessly crushing them. Maybe next time you'll be more careful before randomly destroying things.
The Mireclops in 3, his "tells" are very subtle and rely largely on audio cues, his feet push the bog you fight him in down, making knocking him over very dangerous if you don't use blues, his big attack can, if you're unaware, wipe out your entire army in one go. Even once you have him down and vulnerable, his massive tongue sweeps around him in a full 360, and when he gets low, he'll do it several time. Regardless, his sheer scale and the intensity of the fight makes him both this and a Best Boss Ever to some fans.
The Submerged Castle, with the Waterwraith dropping in if you linger on a floor for too long. There's also the fact that you can only take Blue Pikmin in when the dungeon has all hazards — including the one that instantly kills Pikmin. Luckily, you get Bulbmin to alleviate the problem.
The Wistful Wild dungeons, particularly the Hole of Heroes. It is filled with bosses, and one sublevel is filled with every kind of the most dangerous Bulborbs.
For the Challenges, the Subterranean Lair can cause massive amounts of headaches. It's not a big level, but it has three Spotty Bulbears wandering around, all followed by dwarf bulbears.
The Secret Testing Range. Thought fighting Man-at-Legs was bad enough? Now try it with a timer.
Purple Pikmin to some, due to most bosses in the game requiring quick movement or a Pikmin immunity to beat. Doesn't help they can only be found underground and can't be made with an Onion, and the fact that you need 100 of these guys to get a treasure late game often means most people won't want to risk losing them so they won't have to do as much grinding for them late game.
There's also Ultra Bitter Spray. Although it can immobilize enemies and even make some of the toughest bosses a complete joke, it is much rarer to come by in comparison to Ultra Spicy Spray, and the berry plants needed to farm them are often in inconvenient locations. As such, most players will only ever use them if there's absolutely no other way out. (Usually when they're being faced down by a Spotty Bulbear.)
White Pikmin, when eaten by enemies, release a poison that knock off a large chunk of their health. However, most players prefer not to lose too many whites - although technically to beat the game only one is needed to dig up buried treasure and disarm toxic vents, if you're ultra patient.
Ugly Cute: Some of the enemies like the Bulborbs and Toady Bloysters tend to be this.
Visual Effects of Awesome: The general consensus is that Pikmin 3 really shows off how gorgeous games on the Wii U can truly be. The first two games, though quite old by now and showing their age, were absolutely stunning in their own time.
Though the President is a greedy bastard, if you take too long to raise up enough money, he starts giving you status updates on how he's had to go on the lam to hide from the All Devouring Black Hole Loan Sharks and is now living under a bridge. Keep dawdling, and the loan sharks find him and threaten to bury him in a swamp if the debt is not repaid. His messages afterwards consist of him fearfully begging Olimar to work faster. It's kind of hard not to feel sorry for him at that point.
Jerkass Woobie: Louie stealing all of your food in Pikmin 3 is a serious Jerkass moment from him, but when you realize what he's been through, his actions become more understandable. After having to help Olimar look for treasure just to buy Olimar's old ship back, the ship they used to get to the planet gets wrecked. Even though they're stranded on the planet without a ship, Olimar continues to look for treasure despite how pointless it is, forcing Louie to look after himself. In the end, the only thing Louie ever says is "Food!".
Plus, as a Dummied Out clip found among the 5 Easter EggOlimar's Logs points out, although Louie sent out an S.O.S. after running away from Olimar, he was unconscious the entire time the Koppaites were trying to rescue him. Since he woke up while they were asleep, he thought he was being kidnapped, and since the only other ship he knew of was the aforementioned old ship, even if he DID get it out of the atmosphere, it'd probably not be able to reach Hocotate for a LONG while in that state. It's still a jerkass action, but it's hard to blame him.
Actually, it STILL IS, because after all, he was the one who ate all the pikipik carrots and caused the entire thing to happen.