Personally it feels a little too brick-like, but the layout has potential. I think it needs something to break up the silhouette monotony. I suggest giving it a few outer armor shells/jackets/skirts/whatev. Of course, this is coming from the one who made possibly the most jacketed ship ever, who in no way has a bias towards armor jackets.
Not sure about the armor jackets. The look I'm going for is really the single "sheet" of armor surrounding the topside of the ship (That said, the armor jackets look pure win on the Solaris so I may keep it in mind).
Small indented fringe at the top of the side armor belts with lights in it like the Deimos. (Also useable on the apparent bridge structure. For extra points, don't have it on the back and taper the indent out to meet the regular thickness of the back.)
Not sure what you mean there. If I'm interpreting correctly- I am actually going to put windowed areas in places on the armor sheath (around control towers, near the front, and some in the back), but I don't think they warrant actually indenting the geometry. I'm really going for the 'smooth' look when it comes to the armor sheath, so most of the details are going to be painted on.
Side turrets on raised platforms so if you want to stick with the popup look it's clear that the turrets do not represent weak spots in the armor belt, but are housed in areas that were built over the belt.
The turrets are going to be in areas where something else is behind the armor, and the texture (and some small popup geometry, but not nearly as large as the turret) will indicate that there's even more armor around those areas.