Well, first, I'd start with what they actually released since, as Ruckman said, it was pretty good (whereas, if I were to recreate the nineties disc, I'd have to ditch the whole damn thing and start over).
Drop "When Love Comes To Town" (too many R&H tracks) and either drop "October" as a hidden track or drop it altogether.
Add "Gloria" and "11 O'Clock Tick Tock" (the only two major omissions from the officially released set; they were huge omissions, though).
Also add maybe "Out of Control" or "The Electric Co." (probably the former because it was their first single) because the early stuff is not as well represented as the later stuff.
Also add "Two Hearts Beat As One" and/or "40." The first was a pretty big single for them, the second their definitive concert closer in the eighties. There's only two War tracks anyway.
Don't add any more Joshua Tree tracks because there are enough already. Yes, there are some really good songs on there absent, but a compilation needs to at least try to represent all periods equally if it's to serve as a decent retrospective.
Also leave off "A Celebration." It was a single, but not a very well known one, and it doesn't fit the mood anyway. I'd be a little stunned if the band even remembered they wrote this song.
Use the unedited version of "Bad" (just because the minor edits in this song annoy me more than the major ones in "New Year's Day") and the single version of "Streets" (because it's shorter than the album version and more interesting for fans and collectors than an edit of that version). Keep the "New Year's Day" edit since the full album version would probably kill the flow.
Keep "Sweetest Thing" 'cause I like it.
Shift around the R&H tracks so they aren't all piled together at the end.
No stupid bonus tracks or hidden tracks or anything.
So maybe:
1. Pride (In the Name of Love)
2. New Year's Day (edit)
3. With or Without You
4. Gloria
5. I Still Haven't Found What I'm Looking For
6. Sunday, Bloody Sunday
7. Bad
8. All I Want Is You
9. Where the Streets Have No Name (single version)
10. I Will Follow
11. The Unforgettable Fire
12. Sweetest Thing (single version)
13. Desire
14. Two Hearts Beat As One
15. Angel of Harlem
16. Out of Control
17. 11 O'Clock Tick Tock
18. "40"
2 non-album
2 Boy
1 October
4 War
3 Unforgettable Fire
3 Joshua Tree
3 Rattle and Hum
Well, it needs work, but it fixes the problems I've identified at least. (Edit: Actually, I kind of like this.) Hope that comes out to less than eighty minutes. If it doesn't, I'd (grudgingly) drop "Two Hearts" since War has the most tracks represented.
For the B-sides disc, I'd get rid of all the edits and use the full versions. I mean, geez, it's a disc for collectors, don't give them more to collect. The "Love Comes Tumbling" edit is interesting, though, so I'd retain that.
There are a minor handful of missing B-sides, but I think they got all the best ones. There are also a few songs that aren't B-sides but also aren't album tracks (like "Jesus Christ" and "A Celebration") that are also up for consideration.
But since there's room for more a few tracks, I'd probably add "Deep In the Heart" (to complete all the B-sides for The Joshua Tree), "Treasure," "J. Swallow," and whatever else fits. I really don't think there was any essential material they left off, though. I'd try not to mess with the track order much since it works rather well as it is.