SDOIT easily wins when it comes to vocal melodies. And that remains the most important thing for me when listening to music with vocals. SFAM has quite a lot of awkward moments in that department. I think JLB sings a lot better on SDOIT as well. Production on SDOIT slays SFAM. There's more experimentation, whether that's good or bad is entirely subjective, but I like it.
The way I see it: Disc 1 features some of their most 'complete' and most realized songs. Actually, all 5 songs are instant classics in my book. Then you got disc 2, which basically takes the suite/continious piece of music idea of SFAM but makes it even more symphonic. SFAM is a bit better, but it definately is a very great piece of music as well.
So yeah, SDOIT. It has more to offer, sounds bigger etc. Disc 1 and 2 in succession is a bit too much though. SFAM has the best flow for one single listen, no doubt.