I've been out of town this weekend, or I would have responded to this thread earlier, but here goes:
The original model wasn't the best baseline to start with, so I'm going to try to push you away from it, pull you in various other directions, and probably end up being somewhat aggravating for not saying all these things _before_ you started work
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0. Thanks. The existing model needed redoing, I appreciate the effort, and am hopeful that it will turn out well. Now for looking the gift-horse in the mouth:
1. Ditch the tail fins. They serve no discernable purpose, and they don't look anything like the body extensions present on the 3 existing Aeran models.
2. Your current model is heavily anorexic. Maybe remembering the sense of scale will help - the main body of this vessel is going to be (assuming basic shape doesn't radically change) >= 1 km in length. It needs more bulk. adding thin fins, like the one on the belly, is not conducive to increasing meatiness, and, again, runs somewhat off from the existing body projections of the 3 base craft, which tend more towards wedge shapes than fins.
3. again referencing scale - those projections in the front, in the original model, were the spinal gun mounts. In keeping with the mission profile of a multi-purpose (but heavily leaning towards escort duty) cap-ship (as an Aeran destroyer is) the proportionality is off - the gun mounts are too large for the rest of the vessel- it should not be quite so overly front oriented - it's not a giant fighter, nor a special purpose assault craft. Fortunately, as they were just gun mounts, you're entirely free to move, delete, or otherwise modify them.
4. continuing the above, there are some things that are not clearly present - docking, well defined places for turret mounts, missile/torpedo launchers, and (until it gets bulked up) storage space for said missiles/torpedos. The docking issue isn't one of it carrying a complement of fighters (it'd be carrying shuttles, maybe a few probes and such), but more of a sanity issue in terms of the logistics of resupply (having to resupply at stations is a bad feature for something capable of use in offensive maneuvers) Speaking of logistics, it'd be nice if there was room for fuel for some nice big (and slightly more heavily housed than in your model) engines (if you wish to keep similar engine aesthetics to the fighters, you might examine their curves and tapering - but you're also free to do something different) the proportional size of the engines should convey that, for a ship of this size, a larger than perhaps expected amount of thought has been given to acceleration.
5. For extensions away from the body of the ship aerodynamics are to be completely ignored. As said before, it's at least 1 km long. It's not designed to make frequent landings planetside - that's what dropships and supply shuttles are for. The best example to glean from is the aelar, with its thick, solid, wedge-shaped hull extensions, all of which are used as places to put weapons. The curves on the 3 good models tend to be gentle, some of the places on your model are rather sharp.
6. I think, as you bulk things up, you might want to change the shape of your "wings" and make them decidedly less wing-like. However, I think changes in this direction will come as a logical consequence of bulking up, and aren't interesting to discuss until a new shape has been given to the "torso" of the vessel.
7. The unit file is not fixed in stone, do not use it as requirements list with regard to weaponry. It makes some reasonable suggestions, but it's too front oriented at the moment, as the previous model was heavily front-oriented.
If I seem overly picky, ornery and cranky then it's probably one or both of the two following things:
A) Unlike the humans, who have the myriad subfactions of the LIHW to ascribe ship manufacture to, the aliens, especially the Aera, are going to be kept to a fairly tight set of craft, so if something is not sufficiently becoming the Aera ship it was slated to be, then there's not nearly so much room to make use of the art anyway - so I'm going to be very picky, even though I'm a rat-bastard and haven't actually written the descriptions/made sketches for said ships yet... (notably, I've mentioned before, and I'll mention again, if you want to do a particular ship, you can contact me and request a description - note that while this seems a particularly onerous bottleneck, the idea is to establish a body of representative work for each of the factions under intense and constraining scrutiny so that future submissions won't have to ask what the aesthetics of a particular group are - but we're clearly not there yet, so... I'm staying in stickler mode)
B) I'm awake and writing this right now(more or less right after getting back from a trip, as opposed to several hours from now when I'm happy and rested) because it's too hot for me to sleep.
Admitedly the wings aren't super aeordynamic but they do taper in the front and back as real wings would, Also I think this was discussed in some other thread that the thrust would more than likely make up for some of the lack of aerodynamics. Alos there are far less aerodynamic looking ships then this one. 
So yea. Texturing it is a pain but I'm almost done setting up the UV's then maybe I'll get a little texturing done tonight, if not I won't be doing anything else until friday, got some vacation away from home coming up. w00t.
