I always saw it as some of the differences were because of budget, but at the same time I could also see the Enterprise going through some major upgrades over its years of service. One could even theorize that the Enterprise even went through additional refits prior to TMP. This is not uncommon in navies now, and I think that the articles linked above do a great job of demonstrating how US Navy ships have undergone dramatic changes.
Why would Starfleet do that? Well I have to think that despite the technological advances of the next 300 years, there still a bit superstitious about ships and the Enterprise has been a beacon of success for Starfleet. Why decommission a good thing? Its a luck ship that always seems to come out of incidents ok. Not like many of her sister ships which are destroyed throughout the TOS.