Troika, but I've always felt that the reason for their financial failure had more to do with outright bad luck and very poor publisher partnerships. If they had better support from the publishers - every single game they produced was rushed and they never had enough time to finish their games.
This is basically what happens to Obsidian as well.
LucasArts moved up the XBox release of KOTOR2 a few month in order to have the game out for XMas. This forced Obsidian tu cut a lot of content and when they wanted to create a content patch to restore it, LucasArts didn't let them.
Neverwinter Nights 2 had a tight schedule, but I think there were some issues during development as well so Obsidian has their share of blame, and at least Atari let them patch the game properly.
Alpha Protocol is a prime exemple of a publisher dropping the ball on their developpeurs. Sega basically offered NO support, they didn't even bother localising the game for foreign market either and the delayed the game for six month AFTER the game had reached its initial released date, without communicating one bit about it. These six months could have been used to properly polish the game, do some balancing or bug fixes... but Sega didn't let Obsidian do it and just that on the game until the release they had decided to change for no reason. (As I recall the exact same thing happened with Sierra and Arcanum - indeed Arcanum actually leaked a few month on the Earth, it was buggy and people were "Well the final version will be improved" but as it turned out the copy of the game that was released ended being the same buggy one that got leaked a few month earlier).
Regarding Sega they also cancelled the Aliens RPG, and we still didn't get a reason for this. But then they seem to be handling the Aliens IP like crap, just look at the development of the Aliens Colonial Marines FPS... Though to be fair the cancellation of Aliens Crucible is what allowed Obsidian to rebound by doing Fallout New Vegas by the same Team.
Bethesda didn't exactly screw Obsidian and AFAIK they were very supportive... but Obsidian had a *very* tight schedule for Fallout New Vegas. They basically made the game in 1.5 years (I'd LOVE to see Bethesda try to do the same), and this is very short for a game this scope, with so much choice and consequence. The game is criticized for its bug, but it's a wonder it worked that well upon such a schedule.
However you know what game was made with strong publisher support, with a comfortable schedule ? Dungeon Siege III (which might get bashed by PC gamers but was a great Dark Alliance clone in the end), which also used their own engine, and which ended up very stable and pretty much bug free ont all three platforms.
Regarding the choice of Projects, one gotta point is that Obsidian probably doesn't have much choice: they WANT to do original IP and games, they've kept bringing up new IPs to publisher but they are just not interested. The thing is, getting a new IP started is just HARD. It's a risk and publishers are warry to take that risks, even moreso for RPGs. Even Bioware shipped Dragon Age for years without finding a publisher for it even while ridding on their previouses successes - indeed they only DID find a publisher for it... when EA bought them! It might be exagereted to claim that without EA Dragon Age might have handed cancelled and never published... but it IS a possibility.
In any case this is worrying news for Obsidian, I hope they recover, and I hope they'll have new projects to work on soon.
-Sergorn