With Neal's vast body of work between his solo/NMB stuff, SB, TA, and other projects, he should be expanding his set lists to the point where anything could be played on any given night, instead of full album performances or static set lists. It would be pretty interesting if he committed to that, even just for one or two tours.
Well, he has played music from his various bands with his other various bands, just probably not to the extent you're wishing for. For example, he's played SB tunes (in full and in partial) with Transatlantic, Flying Colors, solo, and with the Neal Morse Band. He's also played TA tunes with his solo tours and with the NMB. I think what it comes down to is wanting to represent the music he's recorded with the musicians he's currently touring with. Granted, Portnoy is in like all of those groups, but each group has different lead vocalists (Roine & Pete, Bill & Eric, Casey) whose voices all lend themselves to their music, but hearing, say, Bill belt out Pete's lines from Transatlantic, or Casey sing some Transatlantic, might feel a bit weird.
If Neal had a MEGA tour with all of those musicians on stage, he could probably do it justice, but I don't see that happening at all. Now, if it was just music that only Neal sang on, that would be more likely, especially since he does that already with Spock's Beard songs (and has been doing for the last 20 years).
Maybe when Neal feels like he's reached the end of his live performance career, he'll hold one more Morsefest and feature music and musicians from all of his bands (SB, TA, FC, and NMB) and have a week-long concert festival.
-Marc.