Having said it in other places, I'll be brief. I agree with the "What the hell?" sentiment for TUC's end overall. I was loving the first half of the book, but as soon as the attack on the Ark begins, I was feeling a bit let down. I was expecting more of a look into the Ark and Golgotterath itself, more of what the stories and Akka's Dreams had made me envision. We didn't really get any of that; just a lot of fighting outside of it and a look into the Golden Room.
Many of the plotlines that were set up aren't concluded (Crabicus, Ciphrang Assassin, Meppa, to name a few off the top of my head), and that's without acknowledging that the book creates a huge amount of questions at the end without explaining any of them. I think the ending would have felt more satisfying if it all hadn't happened so fast. However, right as you're expecting to get all of the answers, the entire plot turns on its head and the book ends.
Now, I love the way the story concludes by itself. The last line gives me chills. I think ending the story on disaster like this is awesome. I just wish that it had felt more coherent and less rushed. Keeping in mind that this is the conclusion to a series of books, I feel a bit cheated. I think you're going to get this opinion from most people who aren't aware that a third series might be written (Just take a look at the Goodreads reviews- they read much like OP's post and don't seem to know there is a planned third series).
I think if Bakker were to come out and say, "Yes there will definitely be a third series", I would feel better about it. As it stands, I liked the book a lot, but I have very mixed feelings about the ending.