I would definetely go with the customization thing
and it would be awesome if you had to go through every region including Fiore and Orre, you also would have to become a pokemon and such.
It would also be cooler if pokemon could learn, like six attacks, seriously, I think four attacks are not enough,
I also think that the GTS should be changed (not exactlay like stated previously by Psylark) wouldn't it be cool to be able to search for shinies? or maybe to just simply offer up a pokemon and choose the best offer that is given, but if you wanted to you could still ask for a certain pokemon. (you can look at the stats the OT, the attcks and pretty much everything else)
I think that every pokemon should be obtainable within the game. Some other cool feature could be, for example, letting out a pokemon so it can follow you (like in yellow) or maybe having more than one save file/being able to change characters and being able to save the customized ones. There sounld also be a distintion between pokemon when you are surfing, I mean really, in ruby and sapphire it always look a wailmer or whatever.
hmm...I think that about covers what I think