Currently, there is no way of distinguishing between the rebels and the loyalists in both the races [not that I know of, I have looked to see any differences but couldn't find any], if you start the game with randomized factions (as I mostly do). Granted it is not a major issue, I would still like to see something that would help me tell if the enemy I am facing is a rebel or loyalist. Right now, the only way I can tell is when he builds his titan. Since it can take time to build a titan, I want to be aware from the get-go.
Moreover, in this one game I was playing, my ally was named Nathmein (something like that) Rebels. I assumed they were, as the name suggests, rebels. Then he built the Anklyon Titan. Not a big problem since he was my ally, but with an enemy, tactics in approach would be different.
One possible solutions is to indicate rebel or loyal in the Relationship window AFTER the enemy has been scouted. This would allow players to get the necessary info, but only after they have put effort into finding it. Also, assigning AI names appropriately (and avoiding the above mentioned scenario) will make for a better end product.