No trek ship is perfect that includes the original Enterprise
Those words are basphemy. The original Enterprise is perfection incarnate in starship form. To say it isn't perfect is like saying the sky isn't blue. There's just no way anyone can prove something so outrageous.
:looks around for snipers:
Um, I'll field this one gentlemen.
1. The interior sets of the E-Nil doesn't match the exterior models, sometimes not even close. For example, take the windows flanking the shuttlebay observation corridor set. No amount of stretching and scaling can make them line up with the windows on the exterior of the models.
2. The nacelle pylons are too flimsy.
3. The interconnecting dorsal is too thin and has unnecessary windows.
4. The E-Nil's saucer needs a gangway. Just one.
5. This kind of fits in #1, but deserves its own spot in the list. The shuttlebay set doesn't leave enough room for power conduits passing from the engine room to the nacelles via the pylons. The attachment points of the pylons would strongly need internal structural bracing of some kind. There is no room for it.
6. There was never established in TOS a consistent location for the torp launchers. It was, in fact, the main reason this battery was added to the TMP vessel, to remedy this oversight.
Shall I stop or go on?