One reason I never totally bought into the tri-nacelle concept was that Kirk introduced the Excelsior as "the Great Experiment". If three nacelles were better than two, wouldn't Starfleet have built Excelsior to that specification? (Or, for that matter, the refit Enterprise?)
Not necessarily. The Great Experiment was a reference to Excelsior being the transwarp testbed, and at that time it was the first ship to test it in operational duty. The main reason for the third nacelle, as I've often heard it, is to give the dreadnought and other tri-nacelle designs more warp power for the systems and the ability to generate a larger warp field, thus keeping such a large ship reasonably fast.
Since transwarp was still unproven when the Excelsior was commissioned, it would make sense to keep the traditional twin arrangement until the tech proved itself.
Personally, I tend to consider the Star League a small upgraded subclass which some ships were converted to, after the Federation class was modified to movie era specs. So you'd have the original Federations, then the movie refit, and then the Star League refit. The Ascension is a dreadnought conversion of the Belknap strike cruiser.