- Lack of maintainance
If you put something new into your game, it's your job to make sure that it works as it should and not the player's to avoid the bugs it causes
- Fakemon/custom sprites
Especially when you use them alongside other sprites from someone else. If you make a game, make sure, you stick with only one style. Everything else just feels awkward
- horrible balancing
Goes without saying; making opponents higher in levels, just to make the game more difficult, is stupid. All it does is make most people grind their team and grinding isn't fun and engaging. Also, you have to keep in mind, that most people are just too used to the cheese, the main series is known for, so a lot of people can't come up with a clever solution for a given battling problem. :P
- horrible level design
Some of the areas just look incredibly ugly and give off a feeling, that the person who designed them, just wanted to throw out a quick runthrough map.
- lack of atmosphere
It's nice and all if you want to give your game a somewhat dark feeling, but then don't use the default upbeat happyhappy battle themes. Same with all the locations.
- lack of worldbuilding
Bugged me the hell out of Insurgence (I know, it's not a ROM hack, however both ROM hacks and Essentials games suck in this regard, equally). You start off in a hidden Darkrai cultist HQ and make your escape to a nearby town. However, the NPCs didn't seem to care about the cultists at all and instead just repeatedly told you how cool it is, that you get an Eevee as a starter and how to open your menu. Like seriously, there's this giant evil HQ right there, where people die. Why not talk about people vanishing, or people having nightmares (which btw. fits perfectly well with the Darkrai theme, as it causes nightmares), instead of basic gameplay mechanics? Worldbuilding is important, especially when you want to make the game plot driven.
- NPCs explaining basic gameplay mechanics
It works in the main series, because they always try to get new people to the series. Fangames, however, are mostly played by people, who already played at least one main Pokemon game. So, they already know how the games work and you don't need to explain it to them. Even if it's new stuff, they should be able to figure it out on their own.
- multi region features, for the sake of having multiple regions
If the other regions don't expand the game plot as a whole and just serve as a giant bonus runthrough map, then you're better off using only one region and expanding it a little bit for more content.