At the end of the day its a space issue. Back in the N64 days, the maximum number of pokemon models the cart had to hold was 250 or so. We've basically doubled the number of pokemon since then. The NDS is more than capable of handling the CPU workload it would take to make Stadium-style graphics...but would it be worth it if you could only have 100 pokemon in the game? As the years go on, spcae will become cheaper. i predict we'll finally see a fully 3D main entry of the series before the NDS life cycle is out.
Until then, enjoy D/P. If anything, it's showing that 2D games are still viable. God, what I would give to have a proper Street Fighter sequel with 2D sprite goodness.
Mmmmm....sprites.