I actually really liked this arc. It went into the character of Asaaj, into the relationship between the sith, and we got to see lots of cool things along the way; such as Dathomir, all the martial arts, some great lightsaber fights, some awesome brutal moments with Savage.
In my opinion some of the best episodes of the series in terms of atmosphere and execution. The trials the Zabraki had to go through for Asaaj's selection were cool, especially the second one, where Savage and his bros were getting picked off one by one, that was super creepy.
Savage wasn't really a paper-thin character, if you recall at the beginning of the arc he expressed serious concern for his brother, laying down arms at one point to make sure he was alright. I don't get why you think its confusing. Asaaj and the Nightsisters manipulated him with some creepy force juju and turned him into an emotionless tank. Then he is constantly abused by Dooku, abondoned by Asaaj, and basically left on his own. So he journeys back to Dathomir, the only place he can call home.
The thing is, I think this Mother Talzin, the leader of the Nightsisters has private machinations of her own; quite like Darth Sidious/Palpatine. And Savage, instead of being Asaaj's method of revenge or Dooku's weapon, is now her own pawn.
The whole point of the exact ending not making sense is its a cliffhanger. There's going to be a follow-up.