I'm going strictly by the idea that I have to choose five songs, because I really end up loving each and every Dream Theater song I listen to.
"Lifting Shadows off a Dream." I mean, I love Myung, and I really want to hear more from him, but I found this to just.. ah. It's not a very... ear-grabbing song. To me. It's just a ballad that hasn't aged well in terms of the mix. I do love how, for a lot of the song, John Petrucci is pretty much just playing his own thing. :3
"Lie." If this song didn't exist, "The Mirror" would have a proper ending and my playlist of the Twelve-Step Suite wouldn't start off with a prelude that abruptly cuts to static instead of ending.
"The Spirit Carries On," so Metropolis would have gotten a satisfying climax. So Nicholas spends days investigating a murder from a past life in what was basically Inception ten years early, and he's finally gonna get some answers, but then this song shows up. This song, which is almost literally just "Oh hey, don't worry about the murder. Just go home." "Oh. Okay." Then they gave Nicholas that sour grapes justification of giving up, "Oh, I guess it's okay, I mean.. her spirit's carried on, hasn't it?" Instead of this song, I would have loved Nicholas actually.. doing something. A climax. Or, hell, if they had to keep this, make the spirit-carries-on motif a bit more.. y'know, prominent? Maybe change up the ending so we get an epilogue of a next-generation Nicholas, whose spirit has carried on? But I'm nitpicky.
"I Walk Beside You." I mean, I loved Octavarium, especially the actual album (if the title track wasn't the conceptual centerpiece, I'd have put it in this spot), and this song's quite fantastic, but where does it fit into the Octavarium? The song's saying "Hey, don't worry, I'm here for you." ..where's the cycle, the thing the character is trapped in? Hey, y'know what would have been great? If "I Walk Beside You" was replaced with "The Spirit Carries On." That way, Metropolis would have gotten a good climax, and we'd have a proper cycle-based song here. If "The Spirit Carries On" isn't in the right key, I'm sure the band could, like.. write a random interlude halfway through that is. Y'know, make the song progress for once.
"The Ministry of Lost Souls." Like "Lifting Shadows off a Dream," I just.. can't get into this. I mean, the extended instrumental section's nice, but it reminds me of that of "Endless Sacrifice," which.. well, I just preferred it!
..in case you can't tell, I'm not the biggest fan of "The Spirit Carries On." But still. Think about my suggestion. Metropolis ending with Nicholas finding out about the Miracle's secret, then we'd have a third act which would consist of his search for the Miracle. There'd be all these nuggets throughout the act about "Open your eyes" and connections between the Miracle and the Hypnotist, but Nicholas wouldn't pick up on them, so around the end, he'd just go home, defeated. He'd put some music on, pour a drink, sit in a rocking chair, then you'd hear footsteps and "Open your eyes, Nicholas." Whether this would end as normal or with an epic lightsaber duel is entirely up to the band. AND "The Spirit Carries On" would be in Octavarium, while "I Walk Beside You" would probably just be a B-side.
Think about it. >_>