One thing that I've always wanted to see more in the main series, and that I like Reborn and the other fangames here for, is side quests. I like side quests, sometimes even more than the main adventure.
The main series has a few, but they're less common than NPCs asking for trades. I don't consider those sidequests, just a way to obtain a Pokemon that's otherwise rare or hard to find. The kind of sidequests I'm referring to are ones where you explore an area that you otherwise might not have known existed, do someone a favor, solve a puzzle, etc. Ones where you actually do something and/or interact with the environment. I want to put a lot of these in the fangame I'm working on.
@the level cap: whatever the restrictions/consequences are, I've always felt that enemy trainers shouldn't go over the level cap. A single, powerful Pokemon like the giant Steelix is fine, since it's one vs presumably a team and realistically you would come across extraordinarily powerful Pokemon like that once in a blue moon ice cream. But when it's someone like a Gym Leader with a whole team, it just feels like they're cheating. That they can't beat me without leveling past the point where I should be able to. My team in Reborn is in the high 80s, my Rejuvanation team is a little past 70, and I've been overleveled in both games since before the first Gym, so I may be a hypocrite. The player is actually penalized for going over, though.
I've also always thought Gym Leaders and Elite Four should rely less on potions and more on held items. I've always thought battles like those were supposed to be battles of wits, so when they keep using potion after potion, it kills the mood. Whereas held items are very strategic because they're designed to boost performance, cover for one of the holder's flaws, hurt the opponent for attacking a certain way, etc. If you take away healing items for bosses, though, you probably also have to take them away from the player in those battles to make it fair. I personally don't use healing items unless it's a long way back to the Pokemon Center and I don't feel like going, but some people might not like/agree with not being able to use their items.