Honestly, if they were to ever do a series finale I pretty much agree the end should be what you make it based on your desicians.
As far as the whole Obsidian angle goes, truthfully I've enjoyed most of their games. I see them as being sort of Bioware's "B Team" nowadays because they tend to use the same basic engine.
Games like "Knights Of The Old Republic" and "Neverwinter Nights 2" not being finished properly are one of the reasons why they are criticized however (for those who say someone should play those before criticizing). The missing HK factory (KOTR 2), the fact that the entirety of Keira's plan is never explained so a lot of things make no sense (KOTR 2), several chopped plot elements, including romance plots (NWN 2), etc...
One of the big rumors however is that they have been forced to go with earlier builds by the sponsoring company, especially in the case of Atari (who did the same thing to Troika with Temple Of Elemental Evil), this done for censorship related reasons.
I do have some concerns, fearing that either their going to sanitize Fallout: New Vegas to get it published from the beginning (meaning they aren't likely to outdo Bethesda), or at the last minute be forced to again go with an alternate build.
Unrelated to either point the fact that I have not heard of Brian "Mad Dog" Fargo being involved in this is the most dubious sign. Brian Fargo being the soul of Fallout since it was Wasteland in my opinion. Faran Brygo always stuck me as the series MVP.