When there is many I could mention my biggest pet peeves are the use of the 3D pokemon battle models and gen tile set mixing. This can severely break a game aesthetically imo. It's always an eyesore to look at.
My pet peeve is when the intro is whether to short or too long and therefore the "choosing a starter"-scene is too long or too short, it's a shame.
When there is too much lag ingame
too many typos
games that are based on Kanto or Johto, with the old story, old tilesets, like red and blue.
games with gen III -ish tileset.
mixing tilesets or even sprites.
I know that many people who make fangames don't have much experience with pixel art, but it bugs me when an overworld sprite looks different to the trainer card sprite due to the sprites being spliced/recoloured from existing ones, resulting in stuff like the OW sprite and trainer card sprite having different hairstyles. It also really sticks out when the trainer's outfit is just straight up recoloured from an existing trainer sprite's, it really isn't that hard to make some minor changes in Paint. Hell, Paint is more pixel art friendly than stuff like Photoshop for me. (It's mainly because of the very good line tool which PS etc have no equiv of.)
If you struggle with pixel art or are unsure about making edits to sprites then I recommend finding one or more existing ingame sprites with similar features to what you want to draw and then carefully study them so that you can copy the technique. Making the shading style look like the official ones is really important, too. Also, it can be hard to choose colours that look right so it can help to copy ones from an official sprite and tweak them as needed.
This bothers me because I know that isn't true. Even if your game is following a classic format, you have to be making something new with it. Most of the time, I see fangames taking place in new regions, and that means that there's been a ton of new settings and characters involved. You put effort into that and made something new-that's not something you should just skip over.
I had this problem while playing Uranium. The forest was beautiful, the cave ok and then comes the first Gym... it completely turned me off. I can see that it was meant to ressemble the canon games, but it felt empty.
EDIT: Also, having too much cutscenes (demo of Yakuza 6 mainly) and roadblocks at the start of the game is a big no. Really, if I have to watch a full hour of cutscenes before the start of the game, I'm better off watching a movie. Pokémon Moon was slighty better because you could walk between cutscenes, but still...
I debated for a while whether I wanted to post this since it's honestly not that big a deal and it's not anything to do with fan game development but I can't sleep and maybe some other people can identify it so I'll do it anyway:
to all the people I see in the game threads saying "it doesn't work," "it crashed," "me stuck," et al
to all the people I see in the game threads saying "how do you extract zip," "does it work on mac," "how do I start," "what emulator do I need," et al
please learn how to use a computer
(to be clear I think an overwhelming majority of players have the sense to not make these posts but when someone actually does, it can really give you more than a few extra gray hairs)
I'll start off by saying everyone starts somewhere, and I understand that not everyone has acquaintances or the abilities to do certain things. (But even then you can put forth an effort.) Anyways- 1. ,"Oh My Arceus!"- Oh my god or oh my gosh is just fine. Please don't use this in dialogue, silly or seriously. It makes me grit my teeth in cringe.
2. Default Battle HUD. Default Move Animations- This might sounds hoighty-toighty and picky-wicky but if you're not even going to put an ounce of effort into the optics of the majority of your gameplay...well-
3. Anime Tropes/Anime Characters- I know that a lot of people for some reason like demure, sweet, lobotomy-stitched cutesy girls who only care about happiness, friendship, and putting their subservient kindness above all else but please- Let's try to have characters exhibit a more complex femininity. Even if you don't understand women. Also, I don't want to see Attack on Titan or Sword Art Online characters anywhere near me, especially in a fangame.
4. Kanto Starters- I promise someone will still play your game even if you have something else to pick besides the unholy trinity.
5. Maymays- Please don't use memes or reference popular meme figureheads. Please. PLEASE! It is single-handedly the most distracting thing I have ever encountered. This includes references to online comics about, "EYUP! THIS POKAMANS MECHANIC SHURE DON'T MAKE NO SENSE! LOL!!"
If you're tempted to poke fun at a certain mechanic either change it or leave the joke out.
Just do your best. (ALSO! I have never seen a YouTuber in a fangame but that sounds insane. I think I'd have to stop playing after that.
Markiplier has a nice body but he's not funny in his videos so how is he going to enhance your game?)
My biggest peeve, is having towns from the game, such as New Bark Town, or Pallet Town, and changing the layout, and area surronding it, till it's no longer identifiable as New Bark, or Pallet, except with the name you slap on it.
I get it if it's some anime eccentric game, or if the upgraded graphics requires some spacing it.
But it's when everything looks 90% different, and I can't see the original layout anymore.
You may as well give the town a new name too.