If I remember correctly, they killed the D in Generations because it looked "fat and bloated" on a movie screen (which I somewhat agree with). The Sovereign might have been okay for TV. I mean, I've watched FC, Insurrection, and Nemesis on a normal TV, and it looks just fine. In any case, they could have at least mentioned that Sovereign class ships were engaged elsewhere. I often wondered during the later years of DS9 why they never even mentioned the Enterprise. The Dominion War was tightly focused around DS9 because of the Wormhole. Why not have some of the TNG crew make a special appearance or something. I would think it would stand to reason that the Federation flagship would be on the front lines, especially given that it is the most advanced ship in the fleet. I mean, the other FC ships made it in (Akira, Steamrunner, Norway), and they were obviously built to look good on the big screen, yet they looked fine on DS9. I think it was simply the ignorance of the show's writers that left them out. Script writers really should know something about their material.
I think the most obvious reason is that they wanted to keep the "mystique" of the Sovereign for movies, even though it too got the crap kicked out of it in all three of its appearances.