I assumed that the story had to pick up again after the first ending. I was listening to the audiobook and reading on the Kindle app on my ipad (disappointing for them not to be synced like the first book was when it was re-released.) The audiobook read the acknowledgments, which is very rare, so I had a feeling that something was coming. Then I got to Bastille's note and the Kindle app still had hundreds of footnotes to scroll through, so I got very confused, but also happy.
At first, I couldn't tell if that was just a joke or if he was really going to continue the series. However, the more I think about it, along with all the reasons you guys have mentioned, it actually makes a lot of sense. It seemed wildly generous to his fans of him to buy back the rights to Alcatraz, but if he was planning another series, it's still a rare thing, but it makes more sense. I also think that it will be more than one book, both because he spent the money to reacquire the series and because so many more questions were raised by this book. I don't think you'd start expanding the mystery, if you were planning to only right a single sequel.
I must say that I'll actually miss Alcatraz as the narrator. I'm sure he could get annoying to some people, but I re-listened to the series this week, and Ramon de Ocampo does a great job with the humor of the book (I especially liked the way he would interject the footnotes, in a way that had the perfect amount of seriousness and obnoxiousness.) I think it'll be interesting to hear Bastille's voice, though, and see Alcatraz and all the Smedrys through her eyes.
Great book! While I would have enjoyed a true ending, I am glad that we're not completely done with this story.