2D left more to the imagination. In 3D, it's a harder for your brain to not take what you're seeing literally; your brain thinks the Pokemon really are just standing there taking turns attacking each other, instead of it being an abstract representation of the actual battle.

In order for our brain to be able to fill in the gaps like it could with 2D, the presentation needs a major overhaul; we need better animations, better camera positioning, etc.