This is why I believe the Sovereign class was originally intended as a replacement for the Excelsior and not the Galaxy. I doubt that Starfleet would have been working on the Galaxy replacement during it's launch. As the Sovereign is quite a bit smaller it is likely it would have been designed to take on the deep space duties of the Excelsior and not the deep space exploration that the Galaxy was intended for. As the Borg and Dominion threat emerged the Sovereign class was adapted for battle during it's design and then more suited for the Federation flagship after the Ent-D was destroyed, especially as the existing Galaxy ships both in service and being constructed would need refitted for war.
Had the Enterprise-D survived I'm sure it would have been refitted and remained the flagship.
That's just my theory anyway.
I'm pretty sure the Sovereign is meant to be one of those ships that Cdr. Shelby said were "on the drawing boards" during the Best of Both Worlds. It's not a drop-in replacement. It's a new design meant to fill a defensive role that hadn't previously existed.