personally i would rotate the entire rear area (engines i assume) 90 degrees so that they are verticle instead of horizontal. Then I would elongate the same section to make it taller. A tower in the middle of the top of the hull acting like the island on a modern day aircraft carrier, and maybe a dish roatating behind it. Then you'd have something inspired by a hammerhead shark. Or maybe I wouldn't do any of those things, but it still looks like the love child of a Battlestar and a hammerhead shark.
So let's get funky. Build it as two separate models, with the Hammer being one model and the rest being the other model. This way you can take a lesson from star trek, where the saucer section can separate from the rest of the craft. Unfortunately, it has to be placed back together in drydock, so this is a function for use only in extreme cases. But how cool would it be (as the player) to watch the "Hammer" leave the rest of the ship and escape as the main body ends up being destroyed. It can hold a small fighter compliment (maybe two wings), and give it awacs capabilities. Maybe it doesn't need a full drydock for reattachment. Maybe some rear area freighters are carrying the modular bits needed to put together a facility that can be used to put it back together and even effect minor repairs. Now we are talking about building a ship with missions in mind, those freighters would have to be protected, as would the temporary dry dock facility. Now we're talking. This is just scratching the surface. The possibilities are as endless as the imagination here at HLP, which I must say, is formidable. From a fredding standpoint, a model of the craft intact, and then models of the main section and the hammer section. This way it shows up as a single ship on radar, until the time of separation, then you can target each section individually. Model replacement works well. It wouldn't be hard to fred at all.
Or maybe I am sleep depped again.
