The main thing wrong with the battle system in the 3rd games is often it can take a very very long time. Input an attack and then watching the hp diminish and then a status affect, it just takes an ungodly amount of time. Add in the fact that the pokemon don't do too much on the animation side, then things become mind numbing. Thought I played the heck out of Stadium 1 and 2, but could not complete the battle modes in collesium or battle revolution because I thought the graphics were just plain aweful.
For some reason, some pokemon looked awesome, and others looked like absolute crap! I would love an entire 3d experience, but where the battles are just a little faster paced and more animated. I always wanted the pokemon to touch in the latest 3d game but when that happend it too looked like crap.