The most recent Pokemon games, Pokemon X & Y, added a few new and pretty substantial features to the Pokemon series. Customizable player-characters, the new Fairy type, and [i][b]diagonal freaking movement[/b][/i] were all new things that many people weren't expecting and seem to enjoy.
We know Pokemon ORAS is now only a few months away, and they're true remakes of Pokemon RS, which means we won't see much in the way of new features, but what kind of "big" feature would you like too see added in the next non-remake Pokemon game?
[spoiler]I've seen some people on a few sites suggest "Pokemon Fusion", in which you use the DNA Splicer from Black and White to fuse certain Pokemon. This wouldn't work for every Pokemon (just like every Pokemon can't Mega-evolve), but for some you could get Pokemon species only obtainable via fusion. I thought this sounded pretty cool, but if they had too few or too many it might backfire a bit.[/spoiler]
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A laser that shoots out of the 3DS and brings Pokemon to life.