My theory is that although the Constitution refits look nice, Starfleet found them lacking in some way. That’s why Enterprise was relegated to a training ship so soon after receiving a major 5 year long overhaul, why a derelict Enterprise A was available to assigned to disgraced Admiral Kirk on short notice, and why we never see a Constitution in TNG or DS9 despite the Miranda, Excelsior, and Oberth classes still being ubiquitous, with even the occasional Constellation being seen in service.
Venom geek media did a really good video on this subject. His theory was that the change to a vertical warp core over the prior horizontal core resulted in too many compromises. Most notably the way the new vertical core overlapped with the photon torpedo launchers could cause the catastrophic loss of the ship in the event of an unlucky shot.
