HERE COMES A WALL OF TEXT!
On the topic of the 3-D idea, I think that it could work really well. Pokemon XD and Colleseum both worked in the 3-D aspect; although it failed in catching pokemon. There wasn't enough to do for the storyline of Colleseum or XD in the end.
If they create a Pokemon game in full 3-D, with the original backbone it has, it'll survive the transition with flying colours. Critics do say that the newer main games show little difference to their predecessors, meaning by that from the Gym Leader aspect, evil team and Elite Four. So, what I'd also like to see is a more skewed storyline.
There should still be gym leaders, of course, but they shouldn't be a main aspect anymore. The main goal is to stop the evil in the world. This can lead to better character development, more engaging storyline and a fresh pine scent to the Pokemon Franchise.
Oh, there's something I've mentioned before in some threads, but I think the next legendary will have something to do with human relations with Pokemon, or the ancestor of humans altogether. However, that may cause controversy (Or a Pokereligion. =P) I mean, Humans are never confirmed as Pokemon in the Pokemon universe even though that's the logical answer, so why are they there?
One thing that would be cool, is it revamp the Generation 1 and 2 battle cries. I'm not talking about changing them outright, they'll still sound the same, but they'll have less fuzz to them. They'll use the same digital program the '5th' gen will use, but will be structured the same way. The only real difference would be the way the sound effect sounds.
What do you think of that idea?
TL;DR version: Let's focus the storyline on destroying the villains. Oh, and revamp the generation 1 and 2 battle cries to reduce digital fuzz.