Thanks again folks...
Just to clarify some points raised (and you'll have to accommodate some personal opinion and preference here):
There is a shuttlebay.
External airlocks don't have to be obvious, nor do they have to be visible. The docking collars appear in TMP, but where are they in TOS or TNG? As it is, there are modelled and textured details which prove too small to be appreciated. If you examine the TOS Enterprise model, she appears to have little 'doors' in odd places (depending on your interpretation of the details), but they can only be seen at extremely close range, and are otherwise invisible (how much of even the coarse detail can you make out in the model shots you see in unadulterated TOS?). Lower-res models aren't usually built for that level of scrutiny in mind, and in-game those sorts of details are often completely lost too.
I can't recall seeing the obvious escape pods appear until TNG and personally I don't really like them being so clearly signposted anyway. If you want them, use your imagination to figure out where they might be and how they might work.
I don't think all ships need a 'deflector dish' because there are more examples of ships without them than with them. There aren't really any good attachment points for such a dish on this model, and I don't want one incorporated into the saucer like the NX01, and I absolutely hate the 'dish on a stick' solution. I would suggest that TOS era designs (in particular) needn't be so stringently constrained by stubborn convention.
The nacelle houses parallel coils, so it doesn't need to be paired.
The concern of the smoothness of the 'shoulders' was one I shared to begin with. However, I had initially tried using simpler geometry but these efforts looked horribly gawkish. Even flattening the leading edges of this version seemed to make it look worse and so I kept coming back to what you currently see. I may revisit it later, but for the moment, this is the version I'm going with (and since this is still a WIP there's still theoretically plenty of time).
I've swapped out the broken LCD and my laptop is back in working order (hurrah!), but just now, work and real life are inconveniently getting in the way of me making further progress with any of my pet projects.