For some utterly strange reason, XY still use grid-based maps. That makes it easier for RMXP/Essentials games to remain relevant. Of course, demand/attempts for perspective-mapped games will increase.
As for the Gen 6 Pokémon sprites... there won't be any. There will still be icon sprites, of course, which haven't changed since Gen 3 (surely they can afford to paint them in more than 2 colours by now?!), so that's not so bad. Gen 6 Pokémon are going to be fan-made sprites, but that won't put many people off using them.
Any and all graphics in XY are absolutely going to be "de-vamped" and made compatible with RMXP. Eventually.
There's going to be a drive by some people (you know who you are) to overhaul their battle system to look like Gen 6, as if the current battle system doesn't work perfectly fine and is inferior to pictures of a non-playable alternative. I don't think it'll be a huge drive, though, as it seems like too much hassle for someone to recreate with sprites.
Overall, I don't think fangames will change that much. Once some Pokémon sprites have been made, and once new tilesets have been made people will add them to their games; however, from what we know so far, there's nothing remarkable that could feasibly be added to a fangame (particularly one made with the limited RMXP).
Of course, what do I know about making fangames?
It would be nice to see a project start up to make a simple (properly) 3D engine, but I suspect even that is beyond the wit of anyone who cares.