Although I enjoyed the TOS movies for the most part, none of them ever really "felt" like TOS Trek. The most obvious and recurring plot-hole (as suggested by the OP) is of course the fact that the original crew always found some way to be reunited on the Enterprise. This is simply not feasible. People's careers do not work that way. Compounding this is the fact that Starfleet is supposed to be a meritocracy which implies that the key members of the greatest crew should all have had much higher ranking positions and/or ships of their own by TWOK.
For me, TOS ended with the last televised episode. Everything that came after it (TAS, the movies, TNG, DS9, VOY, and ENT) were attempts at manufacturing something that was magical precisely because that magic was the product of spontaneous chemistry and circumstance.