I believe it's currently not possible or would require more modding effort than would feel necessary. Currently Gauntlet's Race Mod and Galactic Civilizations of New Eden are the mods that will provide a bit more variety, along with shipsets and races. We will probably need to wait for an expansion before it becomes an option.

Ok well that's good to know - cheers guys

And yes, I've thought about the fact that there are only so many usable shades of red or green or blue etc - I'm planning a 30 player game and I know it's going to get confusing if there are 2 or more factions with a similar map colour!

On top of what's already been said, you can mod in some colour firstly with 'MapColor' XMLs. The trickiest part is knowing the name of the colours, which I don't very well, but if you can find an existing/template to use you'll be able to add a map style in like ~2 minutes, or more if you're toying with what you can do. It's more than just outline colour too; You get to choose borders, resource lines, trade paths and so on.

For ship colours, any variation of AppearanceDefs.xml has what you need. I know not everybody just mods XMLs when they want, but again if you base it on someone else's you can have your own ship colours in like 12 altered lines. Ship colour, lights and engine.