Thanks for the suggestions so far guys, I'm leaning towards the elongated galaxy style, but am not sure yet. Feel free to keep them coming.
After spending some time on Skype with Adonis, I redid the cobra head from scratch. Previously it was too complicated. As a result, the main shuttlebay is now a part of the drive section, and I've moved it back a ways. I've added a small shuttlebay behind the bridge so that the saucer still has shuttles. I've also added details to the nacelles, deflector, and refined a bunch of areas in the mesh. I've also cleaned up the impulse engine housing. The engines are now entirely attached to the drive section, and as you can see, when the saucer separates, two impulse engines are exposed.