Dear god that's a list that could rattle on forever.
I love the core concept of Pokemon but the games are a relics of by-gone days. Not everything should go, it's not all awful, but there should at least be some braver uses of the franchise, even if they still keep the Gameboy formula going.
Why Nintendo has never done a PROPER 3D Pokemon game I'll never know.
Colosseum and the other one both sucked so they don't count.
The problem is a fear of mixing up their winning formula I would guess, that or a fear that if successful they'd have to put more work into future titles.
The problem I find this that the game has always talked about the friendship and bond with your Pokemon, yet you never use them outside of battle or a free taxi service.
By this point we should really be able to see the critters in the world, interact with them, see that they're happy rather then get told by some woman in a random NPC house.
I suppose things have gotten better with the Stadiums and Concerts etc that let you use your Pokemon in some other ways, but it's still just a math game. I don't normally mind that in a game (in fact, I miss it, seeing as it's going outta style) but Pokemon is one RPG that should make the experience more visceral. More show, less tell.
One thing I also always wanted was to actually control Pokemon during battle. Remember like the old anime? My inner 11 year old self is still unsatisfied.
Generally if they made a 3D game I'd hope for something like Morrowind/Oblivion/Skyrim. Huge open world to just go and explore.
Imagine catching wild Pokemon while walking round in that kind of setting. Yeah. Clean your keyboard off.
Of course, they couldn't do that with...what are we at? 600 Pokemon?
It would be way to much work.
So I'd say cut back to about...oh I dunno...150?
Then just focus on making that 150 DAMN good. And boom. Best. Game. Ever.
But, they wouldn't have 200 new toys to sell to kiddies then, so they'll NEVER do it.