I'm picking a Change of Seasons, not because I enjoy listening to it more (I don't), but because it stands out to me as more of a Dream Theater epic, and a bit more well-crafted.
The thing about Octavarium is the music is brilliant, but it's quite obviously derivative. It's designed this way, and I wouldn't change much about it; I love every moment of it! But by wearing its influences on its sleeve, I think it's a bit lacking in individual identity. Another "problem" is the lyrics. They're not bad, but they're certainly not an emotional tour de force. They're just sort of there. That segment toward the end that's a series of homages to other bands and musicians is cool, but I also feel like it's a flaw. As awesome as it is to hear a Spock's Beard album namedropped in a Dream Theater song, I would rather have seen something else.
The payoff is amazing, and it's hard to complain about the song, but when compared with their other epics, I think it just falls a bit short in both distinctness and emotion.
A Change of Seasons is quite different. There's the obvious: in contrast to Octavarium's bright sound, it's dark and dreary most of the way through. It's much harder-hitting, and also much, much more personal. This is the most important distinction. Octavarium tells five different stories from a fairly resigned point of view; there are nods and winks at the listener throughout and little personal investment. A Change of Seasons betrays so much vulnerability that it can be a crippling experience if you really invest yourself in it. Lyrically, these types of songs are often the best, and this one stands with Kansas' The Pinnacle thematically. It's just that powerful.
I prefer to listen to Octavarium. I think A Change of Seasons is better. There's really nothing I can add to that.