Nothing that I can articulate very well. The song just seems forced to me. The drumming is absolutely stunning, but the riff and Maynards vocals and lyrics just don't do it for me. I like the song. Just don't get off on it like I do for The Grudge, Schism, Reflection.
Also, there are parts of Lateralus that bug me too. Just small things. There are parts of Lateralus that are pure genius, but it's not genius all the way through. Same with all of Tool's music. Sometimes they hit the nail on the head, well...most times, but occasionally they hit their thumbs. It does not detract from my enjoyment of their music, no one's perfect. Well.. J.S. Bach was perfect, but that's another story.

I imagine that everyone has little things about the band that don't do it for them. I think that's why people are so angsty, here. They have put Tool upon a very high pedestal. Their own fault, if they hate the record.