I actually think the battles should be made to be a bit more fluid. So while you're selecting you moves etc, the Pokemon aren't just sitting there waiting, they're having at eachother with simple melee attacks, all being blocked or dodged (because it obviously shouldn't effect the battle, it's just for aesthetics) And when a proper attack is selected, your trainer shouts it out in a dramatic cinematic way, and the Pokemon follows suit.
While a lot of people have idea to move Pokemon away from turn based gameplay, it's that simple gameplay that keeps non-gamers coming back to the series. It's so established as well. It's just not an option, it has to stay turn based. But with my suggestion above, it would possibly look more fluid?
In response to
NovusRex
So in a nutshell I'm thinking you want Xenoblade's fighting mechanics? cuz that really would be awesome!!