I don't think the splitting is an issue, maybe the occasional listener finds on YouTube one half of the song, but in the end it's like Six Degrees... a song? a suite? we all know it's that second disc of the album when we talk about Six Degrees of Inner Turbulence, just like if we read "In the Presence of Enemies", without the part specified, we know it's the whole song.
I don't find nothing really wrong with the song, the first, slow atmospheric section when the dark master melody comes in is quite brilliant, and the end is bombastic as any. Maybe the intro is too long and the final solo section could have been shorter or memorable, but all in all I find it a quite good and enjoyable epic. And live it was good!