Cover over the grills and make it part of the hull and add small windows? Or even large rec deck windows ala TMP? You could make one side a rec area and the other a standard living quarters.
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.
Cover the back and place on top a bunch of covers for some vertical launch system?
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.