I think the 3 things I want most in this series are:
-Clone Commandos (but then who here doesn't!)
-More space combat and certainly bigger battles. I know Lucas Animation was still being set up when they were working on the series/movie, but I'm sure it should be possible in a later episode to have something on the scale of what is seen in the live action movies (if they could make something on the scale of the battle over Coruscant then that would be amazing!).
-Some Mace Windu action. I expect we will see it, but still why have Samuel L. Jackson play a Jedi and not have his character see some action in the related animated series?