The Astonishing works really really well for me, viewing it as a musical. I still think the end is really rushed and could've been developed better, but the rest of the stuff is incredible (aside from a few unnecessary tracks such as Begin Again).
The thing is, as a Dream Theater album, it does not even compare to the others, just because it is so different, both musically and conceptually. So, yeah, I like it when I listen to it as a whole, but I'd never even compare it to the other stuff.
I think the biggest difference between the two "big" DT concept records is that SFAM is a Dream Theater album, but The Astonishing is a soundtrack to a story, composed by Dream Theater. And it's not the same thing.