The only scene that left me feeling unsatisfied was that one where they had the battle at Stonewood. I just thought it was clumsily handled and found it silly that Rian and some of the others didn't at least try actively and intentionally kill the Skeksis who they know were draining them and were responsible for The Darkening.
I get that they had to keep the Skeksis alive to lead up to the event and eventual joining in the movie, but I still think that could have been handled a little more immersively.
I also got a bit annoyed by Seladons betrayal and turning against her family, seemed a bit irrational, but meh... that's Gelfling women for you.