Ok, but to put in those newer systems you first have to take out the older ones. For a new build you wouldn't lose time in the construction removing older systems.
R&D has designed newer systems and a way to retrofit them into an existing space frame, so Starfleet decide's to try it out on the first ship to return from Deep Space following these devoplments. The first ship back just happens to be the Enterprise.
Had the Enterprise returned second it might have gone to the Fleet Museum.