There was a ton of work put into this game. The problem is that is was a ton of undirected work, or work on things that were just stupid. The Executive Producer for the game, Chris Parker (also an owner of the company), seemed to think he was the world's greatest designer ever, and created all these absolutely shitty systems and wouldn't listen to any of the real designers or devs about things that just didn't work. And you can't exactly argue with one of the owners of the company when he doesn't want to listen. He basically took over the game and dictated exactly how everything would work (or not work, as the case may be). The other producers realized this early on and just gave up, leaving Parker to micromanage all the designers and programmers directly.
Sega also was a factor, because they kept changing the design requirements (yes they had heavy influence there), which never gave the producers and designers time to actually decide on one set of features to make and polish. The blame is still mostly Obsidian's because the execution was absolutely terrible, and it was obvious 2 years ago that this game should have been scrapped. Instead, though, they focused on adding still more features and never fixed the ones they already had. That is a recipe for tons of bugs and no polish... as is obvious.
This game was just an absolute failure of production, and it's no wonder that so many of the developers left the company, even after the 40% staff layoffs. I am still happy about some of Obsidian's other current projects, New Vegas included, because they are going pretty well. Their big unannounced project is looking great and is already much better than AP ever was, and that may end up being the game that everyone was looking for with AP.
Sega should have canceled AP instead of Aliens...