HM's should just be abilities, not attacks (or some can be both like Surf and whatnot, but they can be removed normally, and the ability kept). Done.
I also would love if it was overhauled as a game a bit, and maybe reflected the Manga and TV show more, in that the gyms weren't just "bosses" to move on. You had to beat them to do the Elite Four, yeah, but I'd rather they were better than you in most cases, meaning you could just do a tonne of other side-quests or whatever until you're strong enough. That probably wouldn't work very well in practice though.
I'd at least want Gym Leaders to have a bunch of Pokemon for them to choose from, rather than just use 2 or 3 of the exact same.