I don't see anything in there for your character's weapons.
Here is what I've found out so far for getting good results when combining models:
- You very much want to use properly setup materials (relying on uvface textures won't work)
- Multiple materials works well
- Your materials do not need to have a texture.
- You will need two uvmaps
- source map that is be the result of hitting ctrl-j on multiple meshes and will look like a mess, but don't touch it.
- destination map: this will start as a copy of the source map (done by adding a uvmap in the mesh data panel). Tidy this up to get the final layout you wish.
- create a new image in the uv-image editor.
- mess around with your uvmap selection (I'm still uncertain on this part) and (I think) select "selected to active" in the bake panel in the render tab
- Select "Textures" in the "Bake Mode" selector.
- Hit the "Bake" button.
With that, you should have a single texture that is the merge of all your other textures and even diffuse-only material colors. With this procedure, you can produce a texture for models that have no textures, only colored materials, or you can use blender's procedural textures in your quake models.
At this stage, it seems to be beyond automation, but if there's a way to get a nice uv layout for the destination uvmap without editing uvs by hand, then it should be possible.
I need to experiment some more, but it seems baking materials to a texture for subsurfaced models might make the texture such that the low-poly model [/i]looks[/i] high-poly (I'd be surprised if it didn't, since that's the whole point of baking normals).
[edit]I forgot to mention that it seems your source textures can be any mix of resolutions: it seems blender to do the right thing for resampling the source textures into the destination texture.