I said this in another thread recently, but ITPOE Part I is great on its own. Had they released that as just one song and never did Part II, it would have still been great. The lyrics are ambiguous enough in Part I to where it could be interpreted in several ways, unlike Part II, which seems to beat you over the head with unimaginative and just plain bad lyrics, IMO.
I actually like the majority of the instrumental section in Part II, though. The beginning part has Rudess doing that bouncing keyboard thing which reminds me of the end of ELP's "Karn Evil 9," and Petrucci's solo when the tempo suddenly changes is very nice. Too bad most of the rest of the song is either unmemorable or ruined by lyrics about dark masters.