I don't have a problem with the quality of aCtA/Crusade's score, I just never felt it was a good fit. I mean a piece of music can stand on it's own, but a score needs to support and enhance what's on screen. While in this case it did work quite well in the quieter scenes, establishing shots, etc. it pretty much fell apart whenever anything remotely exciting or dramatic happened.
The battle scene near the end of aCtA caused such cognitive dissonance it was like watching the battle of Helm's Deep to elevator music. In certain circumstances that kind of thing can work ("And the Sky Full of Stars" springs to mind) but it has to match the emotional tone the scene is meant to invoke.
You're right though, Franke's work in B5 was a bit hit and miss early on (though there were some high points) and didn't really hit his stride until mid-season 2. And yes, I agree that on balance, what was made of Crusade were overall better episodes than their equivalents on B5. But then of course to be fair, Crusade was being made with the benefit of hindsight. Not that it made a difference in the long run.