Here is a different angle.
I don't choose if I only listen them musically (including vocals). They are both epic and classic. Lyrics-wise, ACOS takes the cake. It has deep meaning and touching. I really love the story and it's like every note just screams the words. So it's just an "another world" to me.
While the lyrics are more meaningful in terms of subject matter, a few of them in ACOS seem a little amateurish. A lot of them are great, it's not as bad as The Best of Times, but still, I find that Octavarium lyrics are much tighter and better put together.
A Change of Seasons.
The only thing that separates the two for me is the beginning of Octavarium. It takes a while to get going, whereas ACOS is underway pretty much from 0:00. Otherwise, Octavarium is right up there, at no. 2 after ACOS.
I usually, hate long, drawn out intros. I find they diminish songs like Trial of Tears, The Great Debate, etc. But for Octavarium, it's just the opposite, I freakin' love that intro.