I have a lot to say about this. TOO MUCH to say. But nevertheless, here we go!
Gen 1: Gen 1 has a lot of balance issues in general, as everyone knows. Really, certain decisions regarding types and moves just make me wonder what on earth Gamefreak was thinking. Dragon Rage is the only dragon move (with fixed damage). Why? Why is the Ghost type physical?
Also, a personal annoyance is that trap moves like Wrap and Fire Spin are incredibly annoying in this generation because you can't attack while you're being Wrapped. So if the Wrap-user is faster than your Pokemon, then you can get stuck in a vicious cycle. Same with Sleep, where waking up removes the ability for your Pokemon to act that turn.
Gen 2: Several Gen 2 Pokemon are only available in post-game. It's not only mechanically frustrating, but lorewise it makes zero sense why these Pokemon are only found in Kanto.
Also Ghost being Physical is even more ridiculous now that they've introduced moves like Nightmare and Shadow Ball - Shadow Ball even lowers the target's Special Defense! Even more goofy is that the newly introduced Dark type, with moves like Bite, Crunch, Pursuit, and Beat Up, is Special. I don't think I'll ever understand Gamefreak's logic.
Gen 3: I generally don't have complaints about the mainline Gen 3 games. I am sad about the legendaries locked behind event distributions that I - of course - missed out on. You can't get access to things like the Mystic Ticket or Old Sea Map nowadays without cheating or using ACE.
For FRLG, I think they went too far with trying to make the first part of the game an authentic Gen 1 experience. People have already mentioned not being able to evolve Pokemon into forms that aren't in the original Kanto dex, which just seems like an arbitrary limitation to me. You can't even trade Pokemon from the RSE dex until you not only complete the game, but also catch 60 Pokemon for your dex; again, an arbitrary limitation. The 'faithful remake' troubles were here way before BDSP.
Gen 4: I've mentioned in another topic that I think that Gen 4 suffers from Legendary bloat. It's not the only generation with a lot of legendaries, but it will always be the most egregious offender in my head, probably because I don't like pretty much any of them. In particular, it added way too many event/mythical Pokemon, including Arceus who couldn't even be officially obtained in its own origin generation (at least I think that's the case; I know that the Azure Flute was never distributed because "too complicated").
It's hard to come up with complaints for HGSS but I'm going to do it anyway. The phone calls are way too rampant in the remakes, much more so than in the originals. And it's always something goofy like that Youngster telling me how awesome his Rattata is or people saying that they failed to KO a wild Psyduck.
Gen 5: The way they handled Black City/White Treehollow in Black and White is based on the number of days it took you to reach it, which is just bizarre. On my first playthrough, my Black City was a deserted wasteland because I took too long to get there. What a bizarre feature to put in an RPG.
When your Pokemon achieves movie star status in BW2, it gets an animation when it's sent out. If that Pokemon was shiny, the animation overwrites its shiny sparkles. I know there are people who like this, but I can't overstate how much I loathe this. Please don't mess with my Pokemon's shiny sparkles, Gamefreak. Thank goodness it doesn't transfer outside of Gen 5.
This didn't bother me when the game came out, but now that I'm really into ribbon collecting, I'm miffed that there are no ribbons in Gen 5. I'm also convinced that Gen 5 won't get a remake, so there will most likely never be a Unova Champion title. The only upside to this is that at least this means there are no ribbons that are now lost forever because of being tied to the Dream World or something.
On that note, Gen 5 also relied far too much on wifi connectivity type things. Dream World, Join Avenue, the GTS, the medal system - they all tie so much into interactions that are difficult to impossible without an active streetpass and wifi playerbase. I really enjoyed Dream World, and I miss having it available.
Gen 6: Everyone says XY are too easy and I bet they're right but I can hardly remember anything about this game at all. Cities, characters, routes; it's all a blank, despite my generally having enjoyed the game. So I guess I would say this is the least memorable game.
For ORAS, I really did not like the Dexnav sneaky thing. It made me feel like there was no point at all in just catching regular old wild Pokemon when Pokemon with hidden abilities/egg moves/good IVs appear only by dexnav chains, and I just didn't like doing it at all. Then I'll be running around and a shaky grass patch will appear under my feet and then instantly disappear because I had the gall to just play the game like normal instead of sneak everywhere.
Also ORAS is the only game I can think of that just flat out GIVES you a free legendary (one of the Latis) midway through the game. Catching legendaries is probably my most disliked part of any Pokemon game, but there's just something inherently insulting about having a legendary with a mega stone plopped into my hands when I haven't even beaten all the gyms yet.
I also dislike pretty much everything about the Delta Episode.
Gen 7: There is a lot to fuss about in this generation. Of all the gens, gen 7 felt by far the most insultingly condescending. It also has my most disliked player character design. The festival plaza is a downgrade from Gen 6's PSS. Isle Evelup is a downgrade from Gen 6's Super Training. Wild Pokemon constantly calling for help make wild encounters more annoying than ever before. I also think this generation has the weakest shiny animation; I'm just not feeling the big Kirby star in lieu of the more traditional sparkles.
But I think the most annoying thing of all is Rotomdex, especially in USUM. It is constantly telling me I need to save (right after I've saved) and just hogging all the bottom screen space doing nothing other than being needy. It doesn't help that the roto lotto powers are quite useful so I end up feeling compelled to click on its stupid little sad face all the time and thus enforcing its bad behavior.
Gen 8: Dexit

I know Dexit is not just a Gen 8 thing, but it started there, so Galar gets the blame. I also particularly hate that the GTS was moved to the Pokemon Home phone app; I can't even access it on my Switch, and for what reason? I think you also need a premium account to use it, too.
SwSH was not
quite as insulting an experience as SM/USUM, but it was very close. Even if they want to say that these games are primarily made for children, nobody - children or adult - actually wants to be told to go run along and play and leave the (bad) plot to the adults. In that regard, the Darkest Day plotline was forced and Rose's motivation made no sense.
Bringing back breakable TMs is a decision I will never understand.
Dynamaxing is my least favorite battle gimmick. As a strictly storyline thing, it's a cool concept that fits the theme of Pokemon as a spectator sport. But mechanically, I hate pretty much everything about it.
I feel like Gen 8 introduced a Pay To Win element to Pokemon. Do you want to win with Urshifu and Calyrex? Better pay up for the DLC!
Dynamax Adventures takes the cake as my least favorite thing about this gen, though. I can sort of appreciate being able to shiny hunt legendaries (even though it canonically makes no sense why they're all here), but I really don't like modes that make you utilize rental Pokemon, and the horrible NPC AI makes it a really unfun experience.
Gen 9: The performance and framerate issues are unacceptable. This game generally looks quite a lot worse than older Pokemon games; even SwSH looks more appealing, IMO.
The Pay to Win stuff became worse in this generation with Walking Wake and Iron Leaves being available only for limited time blocks. This would not be such a big deal if they were mythical Pokemon, but they aren't; you can use them for battling in formats where paradox Pokemon are allowed, and they're good, too.
I do not like Paradox Pokemon at all. I find myself more picky about Pokemon ever since Dexit was a thing, and now we've got 22 dex slots taken up by redesigns of Pokemon that already exist. It would be better if they had been regional variants because then at least something like poor Delibird could get an evolution, but no... Plus they muddled up an otherwise surprisingly good story with ridiculous multiverse nonsense.
Everything related to Snacksworth was a mistake. They clearly thought they were being funny turning legendary Pokemon into a big joke. You can't even shiny hunt them. And their IVs are messed up too (because of course they are).
Why am I forced to take pictures in selfie mode when my rotom phone can float?? It's like they thought that having all player pictures be in selfie mode was something that everybody would actively want over other options or something.
I don't like having to 'farm' Pokemon parts for TMs. It's weird and mean and completely unfitting. In most RPGs, you're taking trophies from hostile monsters trying to do you harm... but this is Pokemon. This is a world where people and Pokemon live in harmony! Now excuse me while I go hunt these wild Pokemon for their tears and sweat. On that note, it's kind of a shame to encounter a swarm of wild Pokemon you like and want to shiny hunt because of this, which was never a problem before. In the old games, random encounters seemed like you were getting jumped by aggressive wild Pokemon. Now most Pokemon just sit there not doing anything and YOU have to be the one to start siccing your trained Pokemon on them to cull their numbers until you get to the right place in the swarm to start searching for shinies. It's a brutal world.
Whoever made it to the end of this novel... thank you for reading.