When I read Wicked I hated it. I stopped reading at one point and it took a while for me to go and finish it.
What I disliked the most was Yackle. (I could not remember her name and I find it hilarious that the Wikipedia article drops her entirely).
And, yes, I do like the musical better, but not because it is 'happy.'
In the book, the Wizard of Oz narrative happens because of Yackle. Every time it might go off course, every time Elphaba or the people around her might be happy, Yackle intervenes. Yackle makes the story happen. While some actions do feel like a natural extension, nothing in the book really feels inevitable.
In the musical, though, it is inevitable. Take off the very end and you have a tragedy born from strong, incompatible morals and goals.
(Also, I hated the Philosophy Club scene which felt completely shoehorned in so that everyone was traumatized and miserable. Maybe now I'd see a reason for it, but I read this nearly 20 years ago and I've zero desire to ever read it again.