The UEF as a whole seems like it would be fairly easy to team color., except for maybe the Solaris and some of the utility vessels. Team color-able fighters wouldn't really be necessary, as the Drive trails would be more than enough to identify them by, unless you plan on making the trails nonexistent.
The GTVA would be a bit more difficult. The newer-generation capships could probably just have random stripes added to them without making them look too wrong, but the Orion is a whole other story. And I have no idea how you would handle Vasudans, assuming they show up anytime soon.