It's pretty likely that the queen is going to die before the end of the series, especially if Total Victory is the canon ending. I don't know if you can get that ending without killing the part of her soul in the Tower of the Nisse. It would be really interesting if there's a power struggle for the throne in 3 or if your decisions end up shaping what happens to Haven at the very end.
We're almost certainly going to see the second failure next game, but things like your reputation will likely carry over and I'd be surprised if the faction choices didn't have an effect.