I'll be dividing this post into groups of games, but in all honesty, I haven't been able to stick with and beat a new Pokemon game since Sword (which took me a long time to beat because of university and other factors). I also want to preface this by saying I will not be going over every aspect of the games, only the negative aspects. I know that sounds unfair to leave out the excellent presentation of LGPE, but the title of this thread is explicitly about the negative aspects, so I don't think people are going to expect me to review them. This is not a review. This is not comprehensive.
Pokemon Let's Go Pikachu and Eevee (Gen 7 Kanto): I've played and beaten Pokémon Let's Go Pikachu because I loved the movie Detective Pikachu but was not ready to dive into the spin-off games. I did decide recently to double dip with LG Eevee because it was on sale for $30 instead of the usual $60, but I haven't played that version just yet. The game is too simple and easy for me. I understand taking away Natures, but there was no reason to go all the way back to Gen 1 levels of complexity. Held items and abilities add a lot of complexity to the gameplay, and I don't like that this is removed. Also, I kind of agree with the above reply that not having the option to play with the Pro controller for Switch is a net negative.
I heard Alpharad defend the game because Wild Battles allegedly weren't fun, but I actually feel the opposite when it comes to catching wild Pokemon. I don't like swinging a controller in the same minigame the whole game. I'd rather the process of catching a Pokemon not feel like a completely different game.
I gotta talk about Yellow for a minute. Pokémon Yellow isn't an awful game (or arguably, it is considering Gen 1 is held together by duct tape). It's just kind of a bad starting point for the series and not just because of Brock though that is a big factor. People look at Yellow and say, "Oh, I get to start with a Pikachu like Ash, and I can catch a Pidgeotto early and get all the starters." You're not going to have Ash's team because you're not playing with Ash's OP Pikachu! You're stuck with an unevolved Pikachu (with no light ball) for the whole game. So I understand why they buffed Pikachu's stats and gave you access to some completely OP moves in Zippy Zap, Floaty Fall, and Splishy Splash (plus Pika Papow which I didn't know existed). I also understand why they gave Eevee the choice of 3 out of 8 moves based on the Eeveelutions to make up for the fact that you can't evolve Eevee (which is normally the entire point of getting an Eevee).
I don't like that the games hand you all three starters especially on repeat playthroughs because in that case, I feel like the game has decided 2/3 of my 6 party members for me. I understand you can just choose not to use the three starters, but you're still kind of encouraged to, and this selling point isn't all it's cracked up to be. Plus, you only need two of the starters. Charizard isn't very helpful in Gen 1 singleplayer or even Gen 7 Kanto. Having an electric-type and a grass-type on the same team is normally not really necessary (albeit, Dark-type and Steel-type didn't exist in Gen 1, and Ghost- and Dragon-type Mon barely existed, etc., so it's not as big a deal in Gen 1 or even Gen 3 Kanto with <151 Pokemon to choose from). Which one you need is a bit complicated--because Bulbasaur (as a starter) is recommended for the first three gyms, but an electric-type is recommended for Elite Four Lorelei. With my original playthrough of LGPE, I struggled figuring out what to teach Venusaur, and I was unmotivated to even bother teaching it anything besides grass-type moves because I was just mowing down every non-boss trainer.
That's the main thing. Nobody really challenges you until the end of the game unless you're doing a challenge run. I think even the Elite Four in this game isn't that hard. Red's probably hard, but the post game forces you to fight trainers with only one species of Pokemon between the two of you (good luck getting multiple Alakazam to use by the way), so he might as well not even be there (especially since this timeline's Red didn't do anything--he's not the champion, and he flat out did nothing to stop Giovanni). I don't want to beat a dead horse here, but the game's just ... really too easy because Game Freak really wanted the Pokemon Go players to give the title a chance and stick with the main series, and that just didn't happen. LGPE is an awkward waste of a Kanto remake as a result IMO, but I want to give it another chance with the Eevee sometime.
Pokémon Sword/Shield (Gen 8) Sword is the one I have the least criticisms with ... except for BDSP which I haven't played enough of to have a solid opinion on (other than the fact that the overworld is ... really ugly ... because they saw Link's Awakening and thought "Oh, we can do that as a compromise between the old graphics and the new artstyle" and then the devs didn't have enough time to make it look anywhere near as appealing). Gen 8 is a little too easy, but it's mostly fine. I think the story gets boring around Gym Badges 5 and 6. I'm not going to talk about Dexit because I'm over it by now, but I think they could've put more time and effort into these games. Or at least I would say that about Sword, but Covid19 happened, and I feel like delaying the game until spring 2020 would've been a terrible decision for various reasons that I don't want to get into. No one at TPCi could've predicted it, but that's the hypothetical.
Pokémon Scarlet/Violet (Gen 9): I think I just don't like open world games, so it's a little hard for me to criticize this fairly. First, I will say that "You can challenge the gyms in any order you choose" is only technically a true statement. I don't want to promote a ROM hack here, but people have made ROM hacks where the player can pick any gym leader first and have a balanced challenge (as opposed to getting massacred because they fought the Psychic-type Gym Leader before their starter evolved). I also don't like that I'm encouraged to wander around, and then I wander too far and nearly get eviscerated by a high level fish because I was stubborn about not running away from it. I also don't understand why the Tera type is only "once per trip to the Pokemon Center" in the singleplayer. Like, genuinely, I don't understand. Are they afraid I'm going to cheese the AI trainers too much?
So my main problem with the game (which is probably not how most players feel) is the gameplay loop: I boot up the game after months. I catch some Pokemon and gradually move closer to the water-type gym leader. I get bored. I turn off the game. I think about the game every so often for a while and think "Man, I didn't make any progress last time." I eventually think about the game less and less until the cycle repeats. Recently I've gone months without thinking about touching the game, and I don't think I'll actually complete it. I don't like that I have to go hunting for the five trainers on each route. I miss the trainers challenging me because my character doesn't wear shorts or because they're a sailor on a cruise ship or because they had nothing to do while riding their motorcycle. Catching the wild Pokemon is fine, but I've just lost interest in completing the game.
Also, you know, the game was bugged out the ---, but I don't feel like covering that. We all know that already. Interestingly enough, I only experienced one game breaking glitch. The game got stuck on a NPC's dialogue, and I hadn't manually saved in a while, but thankfully, there was a cheat code to go back to an autosave point even with auto save turned off.
One last complaint is the credits song is by Ed Sheeran, and after months of "Shape of You" and "Thinking Out Loud" and several other songs, I just never want to listen to his music again. Everyone online was upset about it. Patching out the Ed Sheeran song was the 1st mod available for the game. It was kind of funny honestly.
To be clear, the Switch games are fiiiiiine. I'm just ... not really a fan. Sorry for the long post.