Since so much would have been required to alter the first ship design per Jacks's suggestions I decided to start anew and viola! A brand new ship design. It's 1057 polys for the first LOD and 4165 in the smoothed out version. The two fins are for some long range turrets while all the other flat pieces that are visible (under the docking bay and wings in the third picture, in front of engines and top of wings in the fourth.) are also for turrets, the small winglike nubs to either side of the dockbay projections are missle and torpedo launchers, I was planning on texturing that in unless I get told to actually model the little holes for them.
I know that Aeraean(sp?) ships are suppoused to be pretty much seamless looking and the trrret spaces are flat as place holders so I know whee to put the custom turrets I plan on modeling later on tonight. So yea, you know the drill, lemme hear your thoughts everyone. 
), but perhaps you've made it a bit too wide? or, rather, more that it is in particular too wide at certain points - you've altered the tapering shape, having it remain wider until going to the same sized terminating point as opposed to making the structure have a more similar form but be just more substantial in being in all dimensions thicker (including the size of the terminating end point)