I agree that this album does seem quite disjointed. I feel like Keene was trying too hard to be progressive and weird which is why there are so many random samples and sounds being tossed around. With that being said, I still think it's a pretty great record, and songs like Accelerated Evolution, The Eidolon Reality, and Deconsecrate (besides the weirdo circus music) are right up their with some of their best material. I also really like the Cynic vibe in some of the riffs and solos.
I feel like this album will continue to grow on me the more I listen to it, but it is in no way better than Planetary Duality.
EDIT: Does anyone else miss the spacey vibe of Planetary Duality? I thought they did that sound better than anyone and they pretty much ditched it on this album.