Maybe Thunderstone Advance is considered a different property than Thunderstone? Maybe we'll get a real app, like Nightfall, for this, instead of the poopy Facebook-linked app released today for Thunderstone, with the old version of cards and game play?
They should catch up to the new cards in a few months to what, a year at the oustide it would seem based on the pace so far (I've been with them on facebook since almost Day 1, and it seems like they were getting an expansion (several packs) released in about 1-2 months). As for facebook, well, that I can't help you with. But I do believe that Zabu has the rights to TSA as well.
They can't be unaware of the feedback that people don't like Facebook, so it's possible that they'll listen. Hard to say... some companies are really great about listening to customers and others aren't. And then you can have situations where they could say "we'd really love to put this on gamecenter, but it will take us another 6 months to rewrite the code." So yeah, lots of possibilities there.