Now that I think about it... Jedi certainly got their day in the sun with this line too... Dooku, Agen Kolar, Ki-Adi Mundi, Kit Fisto... They're all equal quality to the Clones really.
I'm torn. I have no favorite in the ROTS, I just like the vast majority they've put out. Even Mas Ameda's a REALLY nice figure. It's much easier to point out what sucks...
Right now, my "worst" list would maybe have the Wookiee Warrior basic ROTS figure as the worst. A terrible figure really... Mine even are a paint to get to stand because some dickhole decided that bent ankles was a good idea... Smooooove.