I like the structure of the book better than I do the musical, I think. The musical very much plays out with its focus on Percy in a very linear fashion. Look, this is Sir Percy. He is upset by the French Revolution. He becomes the Scarlet Pimpernel! He does his best to help save the day! He finds himself in trouble! Musical climax! The end!
You mention the twist in the novel, and that's what I love best about it. It feels like there's actual revelations to come about in the way the book is laid out. The answers aren't tipped into the reader's lap off the top as they are in the musical.
What changed between SP1 and SP2? Well, they restaged the entire thing and fussed around with the order of the scenes and songs. They brought Storybook forward and turned it into the opening number with Marguerite performing it as her last performance at the Comedie Francaise. Vivez, Only Love, Believe, Lullaby and You Are My Home (as it was sung between Armand and Marguerite) were songs that all got the axe. You Are My Home became a Marguerite and Percy song for their wedding, replacing Believe, where I'll Forget You replaced Lullaby and the original You Are My Home in the prison scene.
Basically every major musical number was reorganized or rechoreographed and a lot of the dialogue was restructured, especially the sequence following Into the Fire, where the League makes their first set of rescues, the Prince's Ball, and the duel from the second act (which now includes Marguerite fighting rather than standing on the sidelines).
Grappin as a character was introduced in SP1 as Grappin and the reveal of who he really is was something that came about at the end of the show, whereas in SP2 we're shown who he is from the very beginning an there is no reveal.
And in SP2, the League sings a reprise of Into the Fire to a disheartened Percy, which is actually one of my favorite parts of the show. So that's change I can believe in.
Also at the time, Christine Andreas and Terrance Mann were replaced with Rachel York and Rex Smith and the music for Chauvelin was transposed up to suit Rex Smith.