"WTF" is exactly the reaction I had upon watching the ending of this movie a couple years ago. It reminded me of the ending of Majora's Mask, when everyone thanks you for saving their bacon and then you just... kind of... leave.
I seem to recall the Prince actually being mentioned at some point(s) before the end of the movie - I even remember knowing about his being engaged to Princess Peach and some sort of mysterious disappearance after Bowser rose to power. So it wasn't completely out of the blue, but it was a pretty unsatisfying conclusion.
Overall it was an interesting piece of film and I would like to watch it again sometime. Unfortunately, I do not know where to obtain a copy.