Turn the HMs into items (like in Pokemon AshGray), but keep certain moves (cough cough, Surf Waterfall and Fly) but make them normal moves. I think I've seen some people say that they'd remove HMs entirely, but they're an important part of the game. The obstacles keep you from getting into areas you shouldn't go yet. Honestly, why are they even moves? I mean, Surf is kinda cool in concept, and I suppose it makes you put variety into your team, but I just don't get it. EDIT: Oh yeah, and make it so that you can ask a Pokemon to be holding an item on the GTS, like how you can ask for a level or gender, so you don't get jerks who give you a Porygon without an Up-Grade and make you waste yours. Either that, or do away with trading holding items entirely. Oh yeah, and remove limited-time events like Arceus, Genesect, Victini, Darkrai, et cetera. Have the ability to form a friendship with the Gym Leaders. They'd give you their phone number after you beat them, but unlike in HeartGold, it wouldn't just be so you could rebattle them. Instead, you would be able to call them in most or all areas and they'd have something to say, in an Undertale-esque fashion.