Playing around with creating an abridged version myself, here is what I arrived at - trying to balance keeping the best stuff (in my opinion) with preserving the most crucial plot points from the songs and a decent flow. I haven't tried listening to it in this form yet (it has been hard enough to fit in a few listens of the full album) so I'm not sure if there are any stupid song transitions in it:
1. Descent Of The Nomacs
2. Dystopian Overture
3. The Gift Of Music
4. The Answer
5. A Better Life
6. Lord Nafaryus
7. Savior In The Square
8. Three Days
9. A Life Left Behind
10. Ravenskill
11. A Tempting Offer
12. A New Beginning
13. The Road To Revolution
14. Moment Of Betrayal
15. The Path That Divides
16. The Walking Shadow
17. My Last Farewell
18. Hymn Of A Thousand Voices
19. Our New World
Length: 82 minutes
The run of songs up to Lord Nafaryus works well, some of the best material on the album and introduces most of the characters. Descent Of The Nomacs is kept (the sole Nomacs track that is, all others are cut) as it serves as a nice introduction and keeps the flavour of the Nomacs - it could be cut easily enough though.
A Savior In The Square remains, which contains the crucial meeting. My experience was that following on from Savior In The Square, after the great start to the album, things got a little dull - When Your Time Has Come, despite containing the crucial lines ("When you're facing the path that divides...") isn't one of the strongest songs imo, and following it up with Act Of Faythe, while it does a good job of character introduction really slows things down a bit too much. Transfer a little of the content from WYTHC to SITS, and maybe some of Act Of Faythe's to A Life Left Behind, and this part of the album can be done without losing all the pacing (and saving more time for the good stuff).
In my version we go straight from A Savior In The Square to Three Days which is one of the absolute highlights of the album imo. Brother Can You Hear Me is a nice moment, but it is perhaps a bit obvious that Ahrys and the rebels will back Gabriel so I don't think it justifies quite a lengthy track that is perhaps a little boring, imo. Also, since we have cut Act Of Faythe, we now essentially leave the rebels and go back and follow the empire characters after SITS / Three Days. A Life Left Behind is actually not one of my favourite songs on this so far, but it contains too crucial plot points for me to cut in this version, and now serves as our proper introduction to Faythe's POV as well.
Then we move onto Ravenskill and A Tempting Offer, which are key songs for the story and pretty good imo. I like Chosen and The X Aspect, but not quite enough to justify the extra pure character introspection in reaction to Ravenskill and A Tempting Offer.
A New Beginning is a given from quality and plot point of view, while The Road To Revolution and its roundup of character conflicts helps make up for a couple of the cut songs. No need for a recapping instrumental in this version so it's cut, and we jump straight into Moment Of Betrayal. The scene is set well enough at the beginning of The Path That Divides, so unfortunately we lose Heaven's Cove. Begin Again is probably the worst offender on the album for not really adding anything storywise so it is an easy decision to cut, so we now have a run with a lot of momentum coming up to the climactic moment with Moment Of Betrayal - The Path That Divides - The Walking Shadow.
My impression of the album is that once it gets to The Walking Shadow, it seems to have a quite drawn out ending section with a lot of quite similar songs and not that much new added or happening in the story. Cutting Losing Faythe and Whsipers On The Wind alleviates this a bit - we now have My Last Farewell immediately followed by Hymn Of A Thousand Voices where the people rally to Gabriel and help him save Faythe. Out of Our New World and Astonishing, I think Our New World is slightly stronger as the closer so it finishes the album.
Obviously keeping individual songs as they are isn't the ideal way to shorten it, and it'd be better trimming or rearranging certain parts. This was my best effort at preserving the full story and as much of the good music as possible, as well as improving the pacing from my perspective, and getting it almost down to single CD length. I'd do it quite differently if I just wanted to make an album out of my favourite songs without regards to the story.