What I didn't like as much was the way Marguerite was portrayed. In the book, especially, she's the "cleverest woman in Europe" and she figures out who the Pimpernel is long before the final scene. The book also shows us her brave and well-planned journey to France in order to save those she loves. The movie does a good job of balancing Percy's and Marguerite's brilliance: we get to see both of them. Plus, a movie can do close-ups. A musical is limited by its very nature as a stage performance. Nonetheless, the musical does leave Marguerite on the sidelines for most of the action. We do get to see her joining in the final fight scene, which I like. I just miss her being the innocent-and-brilliant actress-turned-lady, center of everything.
Instead, the musical focuses mostly on Percy and gives us more about him than the book does. I loved Percy. He's brilliant at being an idiot, just as he should be. I loved the almost-final scene where he completely takes Chauvelin by surprise. (I'm leaving out details to avoid spoilers.) That was an amazing addition. Also, Chauvelin's character is very different in the musical, due to the plot changes surrounding Marguerite's background. It makes him a lot more evil, actually, and gives us more of his point of view. It also sets up a really cool love-triangle sort of thing.
In order to enjoy different versions of things, I have to separate them in my mind. I love the characterization in the book, I love the visuals of the movie, and I love the music and the humor of the musical. I also like the story of the musical, but I have to love it as a new thing, not as a replacement for the story of the book and movie.