Here's my stab at it:
1. The Root of All Evil
2. I Walk Beside You
3. Another Won
4. Afterlife (was going to go with Status Seeker to shave off some more time, but I don't think that would have gone over well)
5. Pull Me Under (I wasn't going to go this route, but for a 20th anniversary show, it really should be included)
6. Innocence Faded (not my favorite by any stretch, but it is short and fans were happy for the rarity)
7. Raise the Knife (keeping because it was awesome and a rare gem)
8. The Spirit Carries On (I have been burned out on it, but it really deserves a spot)
9. Six Degrees
10. Vacant
11. Stream of Consciousness (Because it is awesome, it would be awesome with orchestration behind it, and I felt that as much as I loved the presentation of Vacant, TOT seemed underrepresented)
12. Octavarium
Encore: Metropolis (great way to end the set)
This was tough. I only made 2 1/2 substitutions: Subbing Pull Me Under for UAGM, and subbing Stream of Consciousness for TAWL and SS. There are a couple of problems with this. First off, I broke the unspoken rule (which I made a rule of this thread) of at least 4 songs from the new album. Second, SS truly was awesome.
But on the whole, to fit the two songs I added, I think this was the most logical way the set could possibly have changed. I just don't see any other practical way. And, honestly, I don't think we lost a whole lot in doing so. Yeah, Octavarium only has three songs. But one of them is 24 minutes (longer, in the live presentation). So the album really isn't under represented. And while this sacrifices a bit on the "Octavarium tour" aspect, it significantly enhances the "20th anniversary tour" aspect. So IMO what was lost on one side isn't as much of a loss as the bigger gain on the other side.
As for not having SS, that was a tough one. But as above, while that is a problem, I think the net gain is worth it. And I was also thinking that, although this wouldn't have helped the concert itself, for the DVD, they could have easily included a performance of the song from another show as a bonus, since it was performed at almost every stop on the tour leading up to that show. That also still doesn't address the fact that the orchestra really added to this performance. But, again, I still think the net gain would make it worth it. If there was any way to accomplish everything else and include the song, I would have left it in. But timewise, it just doesn't work in any way I can see.