I like cross-fades, I think they are cool. But I don't like when a song just fades out, it lacks conclusion. When it fades into a new song, its like it just one long song. The best is like what they did on a lot of SFAM, where the songs fade into each other seamlessly, while playing absolutely fine and having a sense of beginning and conclusion when played alone.
My fist general impressions of this album musically: Overall, it is very symphonic, operatic, epic, etc. It gave me chills several times. I think some of DT's most emotional songs are on this album. I think in many ways this album is piano driven, and it also uses acoustic guitar very frequently- I think it works. But, it gets progressively heavy until the middle parts of Act II, which are the heaviest bits of the album, as the story is the most intense. I think the album overall has a great sense of flow, even without the songs crossfading. I would say it is probably JLB's best performance on an album for a long long time, maybe even since Images and Words. Catchy choruses abound, and the album has a lot of a focus on melody in a sort of operatic way, which fits his style.
I was also impressed by the diversity of some of the tracks. TGOM is anthemic and Rush like, Lord Nafaryus features a metal tango, Three Days has a great groove and a swing jazz blastbeat section, A Life Left Behind has a great, classic prog feeling intro, The X Aspect features bagpipes, and many other songs have either a classic metal feeling, or are piano driven. And then... there's the NOMAC tracks. Don't know what to say about those. But I think its in many ways a very innovative album, both in the little details like I mentioned here and in the overall concept, it just has a huge scope.
There, not a very detailed musical analysis, just some of my first thoughts.