1) I hate the level cap where your poke starts disobeying you. In official pokemon games there is that, but the lvl cap is much higher and normally you dont reach it one way or the other. In fan games in the other hand is a painfull story.
2) The good items are kinda rare or not easily aproachable. Most times thats the fault of specific events which get reset after an epesode or two and you loose the opportunity to do it and earn the chance to get some items which you ll be able to get when the game is complete after some episodes (which means some years probably)
3) the rare revive items. In some poke games you cannot buy in any way revive items which is clearly bad and you loose chances, in gamepley, and precious time that you cannot spent only in a game.