Their whole relationship with Sega seemed to be such a disaster, much more so than anything else they've done, that it is hard for me to believe that Sega wasn't a major contributor to the whole mess.
I wasn't present when they developed it at Obsidian, I don't know who to blame. Plus, despite its flaws, I personally enjoyed the game quite a lot. But you can't deny it's going to be much more prominent in Obsidian's portfolio compared to SEGA's.
I am willing to admit AP is a black mark, even though I enjoyed it a ton, but reputations have a lot to do with what you did most recently, and the damage of AP was almost immediately wiped out by the release of FO:NV. It was well reviewed and it sold very well. In fact, i'd say Obsidian is in their strongest position ever right now.
Now if DS3 does badly, they lose all that.