1) The production - The guitars on IT sound really weird and muffled, one of JP's worst guitar sounds on a DT album so far. The drums are just awfully produced. This lessens the listening experience of IT considerably for me. Octavarium sounds fine in every aspect of production.
2) Vocals - There are some truly cringe-worthy vocal lines by JLB on IT. Notes he just can not pull off. There are no such moments on Octavarium. The vocal melodies in IT are also just very "tame", or "nice". Most tracks on DT12 have that problem.
3) Lyrics - The lyrics on IT is just are okay at best, and horrible at worst. Cliche, preachy, silly, and seems as if just thrown together in an afternoon, with very little thought put into it. Octavarium's lyrics are amazing at best, and completely fine at worst. This is also a problem this track shares with most other tracks on DT12.
4) Flow - Octavarium has a very clear and defined flow throughout its entire length. The opening minutes might drag on repeated listens, but it's at least in the beginning, and doesn't disrupt any flow. On IT though, the extended bit is in the middle, and not only repeats that structure that they only just recently used in TCoT, but brings the track to a jarring halt halfway through. The other shifts between sections in IT are also much more awkward than in Octavarium, where they feel very natural.
5) The orchestra bit - The melodies are nice, but an orchestra with only strings sounds pretty hollow.
Musically, IT contains a quite a few cool ideas, I'll admit that much, but it has sooo many issues that just completely overshadows the good stuff.