Back on to the Ent B. Here's what I like to think.
The ship suffered heavy damage after she broke free of the nexus. She would be in Dry Dock for weeks. But as a sign of respect to Kirk they delayed repairing where he was killed until after the memorial service etc.
Because of all the enhancements made to her and being the only type in service, she was very expensive to repair. These were busy times for the Federation. Their new alliance with the Klingons had stretched their resources fairly thin because of all the aid they were suppling after Praxis exploded. The federation fleet was also rapidly expanding.
So, although superior to a standard excelsior, the Ent B was mothballed until starfleet had spare time and money to repair her. But the the development of the new Ambassador class meant that she was delayed to be repaired. Unfortunatly, after many years, it seemed like she was going to be repaired and brought back into service, the cardassian wars broke out. This also stopped the building of the costly Ambassador and instead more, cheaper Excelsiors were brought into service.
After the war was over, the Galaxy project began. Again taking up many of Starfleets spare development time.
When the dominion war broke out, starfleet knew that they needed to come up with new technoligies. The enterprise seemed like the logical choice to experiment on since she had the potential to be far superior to a standard Excelsior class ship. So they brought the Enterprise out of mothballs and fitted her with many new experimental equiptments such as quantum torpedos, ablative armour
and regenerative shields. She was then recomissioned as the USS Lakota.
If the enterprise was decomissioned then i think starfleet would have planned to recomission her. After all that design has shown to be more powerful than a standard excelsior.