Since the crew would wind up with a front row view of the nacelle end caps instead of anything majestic, I'd choose to skip that concept, even though it is the most workable and logical of the concepts. [...] This holds a bit more appeal, though I'd have to decide what I was going to use the VLS for. My concept is that this is done in the TOS era as a study model of the Excelsior concept, and that it is to be the next generation of front line starship, tasked with the typical multimission role as a Constitution. Thus, exploration, defense, diplomacy, etc. I don't want to overdo the defense side with missile silos, but perhaps atmospheric, oceanic, geological probes... that might work.
IMHO, the Rec room view point wouldn't be terrible, compare it to the officer's lounge in ST:TMP and its not that bad. Nacelle proximity is a possible issue for shuttle or cargo hatch use, unless the doors are on the port/starboard walls, but that's also true for impulse exhaust so it could be ignored. Extra crew/marine barracks ''wings'' as on a FASA Chandley class? Extra labs and sensor space (you could mount TOS upper/lower sensor domes on them)? A combination of shuttle bays and sensor domes would be he most visually radical, I guess. You could use them as something horizontal for a Reliant type roll-bar to be connected to (scratch-built or not). It sounds interesting, and I have designed something not too dissimilar for an earlier era (WIP). Please let us know how it turns out.