Troika Games, which was the gaming company that Tim Cain founded and ran after the dissolution of Black Isle Studios, had been working on a post-apocalyptic RPG in 2004 before they closed down. I believe it had been intended to be a sequel to Fallout, but Tim Cain was outbid by Bethesda when Interplay sold the IP. It likely would have been retooled into something more akin to a spiritual successor, if it wasn't for the fact that Cain couldn't find a publisher and Troika ended up shutting down early 2005.
I don't think that Project Indiana is this same game he had worked on 13 years ago, as most of the assets made for the game are likely long gone, but it does make some sense to me that the game Obsidian is making will be set in a post-apocalyptic world. I'm sure they have many ideas for a Fallout game, and have come to the realization that they will never be offered another chance by Bethesda to make a new Fallout game. It's better for them to have their own franchise that they have full creative control over.
Yeah, I'm hoping it's something as good as FNV, but I'm not sure. From what I've heard about Alpha Protocol and whatnot, they're not great at designing 3d gameplay mechanics on their own. Plus, idk how their writing has held up until now with all the layoffs.