Storyline. Okay, yeah. It's primarily a kid's game. But the story is usually massively oversimplified for those of us who grew up with the original cartridges. Why not cater to older folks for once?
Seamless use of HMs. This is something I've been wanting since RS. When you move onto an ocean tile, automatically activate surf. No confirmation, no animation. It just happens. I mean, how many people accidentally press "A" in front of breakable rocks, the ocean, etc. and then need the prompt to cancel? It breaks the flow.
Better AI. Not much to say here. Make ordinary trainers harder to beat. I want every battle to be a little more challenging and strategic.
Diversify gyms. Each gym always follows an type scheme. How about a scheme based on a strategy? One gym could specialize in paralysis; others, burns, sleep, and so on. Each gym leader would not have to obey strict typing rules and instead organize his team based on a specific tactic.
I like your idea for Gyms. Very interesting. It reminds me of the challenge modes in some of the side games.
I thought the story was VERY well developed and more mature in Black and White. It dealt with some of the moral implications of Pokemon, and that was interesting. Also, Ghetsis was the most frightening villain in the series yet. For one thing, he's still out there. That worries me. I look forward to kicking him into the revolving door.
If you ever have to choose between regular heaven and pie heaven, you should choose pie heaven. There may not be any difference, but if there is, oh boy!