I'll agree that the ship - in my mind's eyes - could've been neckless; instead having the dorsal hull between the aft shuttlebay and the saucer shuttlebay join them in a smooth curving fashion. The front could have matted the seconday hull to the primary by keeping the deflector as is but also framing it in a fashion not unlike the Luna-class which would tie it in pretty well with the arrowhead shape on the ventral side of the primary hull.
Sovereignish? Sure - but I wouldn't care. I think it would've looked gorgeous. I'll agree to the dual necks being the odd bit out that I'm waiting to have grow on me like the rest of the ship and hope it'll justify itself with the way the auxiliary craft will undock or the way the saucer separates. I don't see how they'll do it... but I'm long past the doom and gloom phase. After all, I could accept the Soul Wolf-class in Bridge Commander and find it cool (and the modder even called it an Enterprise too >_> ). IRegardless, it's not going to stop me from enjoying the ship.
Also, I never understood what people meant by 'layeredness' in the first place.