You should look at Sins of a Solar Empire. How it uses its textures IMO is the most effecient. You have the ship UV mapped to a single 2048 sheet. However each mesh uses 3 separate texture sheets. One for the color, or diffuse map. With an alpha channel for team color. The second texture fills the roles of Specular map, Illumination map, Reflection, and the alpha is used for Bloom effects. Each RGB color channel has a separate role. For example the Green channel is used for illumination, The blue channel reflection, and red channel is the specular map. This saves having to use of 4 separate textures to do all of this. Then another separate texture is used for the normal maps. This is all done with DXT5 DDS textures.
Photoshop does have a plugin for DDS format if they didn't finally incorporate it natively in versions beyond CS3. Gimp can work with DDS format, but i am not sure how well.
I would use ether the direct X model format, or .3ds. Most modeling programs can save, or import/export in those formats. Including Blender IIRC. If your model viewer is going to be anything like the NanoFX Evolved viewer. Direct X would be the way to go. Unless something better came out that i am not yet aware of.
I am all for design consistency. As long as it makes sense. In Trek everything on a ship served a purpose. In SFB basically they added a 3rd nacelle, or moved the arrangement around slightly, and called the ship a new class. That is what i would like to avoid. We all know the Federation used similar components on different ships. For example the TMP Constitution, and the Miranda, or the Galaxy, and Nebula Classes. I can live with stuff like that, but the Galaxy X just made me do a facepalm. Don't even get me started on the Alien designs for SFB. Especially the Romulans. What SFC did to the SFB ship designs made a lot more sense. I must insist that any new ship designs must make sense, and serve a purpose, and NOT be put in just because they "look cool". That is the heart of Trek.