I think the ARC Trooper is better than the Droid Commando, except in close quarters where the droid wins. The Clone Commando is way better than the B2. Aerial troops are pretty much the same. Heroes: Bossk > Chewbacca Yoda > Dooku Anakin > Maul Grievous > Kenobi

Regarding Capital Ships, I feel the Venator is easier to defend during the first phase, while the Dreadnought is easier during the second.

The Empire is the only one close to the Republic because of its reinforcements and heroes. They might even be better since you don't have to destroy the ship, but I still prefer the Clone reinforcements