I've been kicking around the tracklisting for a hypothetical Black Clouds/Systematic Chaos combo album for awhile. Best I've come up with, without altering or editing any existing songs, is:
1. In The Presence Of Enemies, Pt. 1
2. Forsaken
3. Constant Motion
4. The Count Of Tuscany
5. Repentance
6. Wither
7. In The Presence Of Enemies, Pt. 2
Comes to about 73 minutes, and flows pretty well too. Having a long epic like TCOT right in the middle could be a bit WTF I guess, but then again, Awake did the same thing with AMBI. Repentance and Wither are nice breathers afterwards, and I always enjoyed ITPOEpt2.
As for the leftover tracks.... I dunno. The Dark Eternal Night has cringeworthy verses, but I enjoy the rest of it. ANTR has Beautiful Agony, and a cool intro, everything else I don't really care for. The Ministry Of Lost Souls would make a cool Lifting Shadows-type song if you extracted the instrumental. Prophets Of War is basically fine, just a bit uninspired. The Shattered Fortress, The Best Of Times, A Rite Of Passage.... Gah, they're all over the place. I don't even know where you'd begin editing all that down.
I would honestly just scrap all these songs entirely (along with Raw Dog.... Fun song, but there's potential for a bit more there), extract the cool parts, and go back to the drawing board. Make entirely new songs, and put together a new album. It worked for Metallica when they were making Death Magnetic, after all (We still like Death Magnetic, right?). I'm sure if some more time were spent in the arrangement department, some really cool stuff could come from it.
Then again, from the looks of things, they apparently just did this with ADTOE (hopefully!). We'll see.