Do people actually make mods for other reasons than editing cap. ship limits? Like adding newer gameplay features? This doesn't mean I don't like the current gamemode, I'm just curious.
Over on the stardock forums, someone posted a capital ship mod that makes all the races' capital ships more powerful, and I think also gives cap ships to the pirates, among other things.
The mod tools (and game itself) have only been out for a short time, so more elaborate mods will probably take some time to appear. But the tools allow for extensive modification of things far beyond the number of capital ships you can have.