Some early RTS games had spy units that looked to your opponent as if they were one of his units (I think Command & Conquer did this, probably lots of others too). On paper these sound like a good idea, but do they actually work? Would they work in the context of PA? Would there be any benefits over using a cloaking system? One potential use of units wearing enemy colours would be scouting, but FA-style scouts might be better for this use. After all it doesn't matter how convincing the disguise is, if you see it come out of the fog of war then you know it's not yours. Another use would be a more active form of intel-gathering. Sneak a couple of disguised tanks into your enemy's tankblob, and have them move around with that squadron. The spy units would have to be controllable by your opponent to avoid them being spotted too easily. The third use I can see would be for sneaky surgical snipes. Take a high-value, high damage unit like a Percival from FA or a Sumo from TA, sneak it into the enemy base, attack something big and expensive. In order to fire its weapons the disguised unit would have to break its disguise. So theoretically you could make a disguisable version of any unit, but there would be a significant cost increase over the standard model. Of course successful use of these units would require an amount of distraction tactics, and I think that more intel-based chicanery is always a good thing.
I've generally found this kind of thing to be too micro-intensive. Having to manually handle these spy units while you're busy playing around 5 different planets would just be too much. They worked in RTS games where you had maybe a dozen units fielded or so, but the scale of this game is too big for anything manual, which means that your units would have to be able to deal with these imposters themselves. Which basically means you're back with some form of stealth/cloak.
While the "fake unit" spy may be troublesome, what about espionage in general? Some features of spies include: Intelligence gathering: An invisible unit is ideal for sneaking around enemy bases taking pictures of stuff. I guess a satellite or plane would also work... but the key idea is that the invisible unit lives for a long time instead of being a 1-shot probe. This is highly dependent on having a "strong" invisibility that's tough to break. Sabotage: Destroy factories, power, sneak past enemy defenses and blow stuff up. Get enough of them, and they can even ambush a Commander. Sneaky sneaky. Theft: CnC spies can steal resources. Perhaps a resource parasite could send goods to your bank? An undefended extractor or generator could end up helping the wrong person. Capture: Invisible captures could end up extremely dangerous and insidious. Similar to Civ type games, the spy would be consumed in the attempt, so you couldn't just sweep through bases. This would need to be carefully done, as unit capture is basically instant death +1.
I quite like how some of the espionage units worked in Zero K, most notably the Scythe. For those who don't know, it's a weak melee unit (the ONLY one in ZK, if I recall correctly) that can cloak. It wasn't too micro intensive to use, but it could have a nice impact on the game for defenders who left wide gaps open. How this fares on a larger scale (cue the people whining about how everyone is always bringing up PA's massive scale) is another matter, as it's a lot harder to catch units like that when you're on another planet.
Once you have UI modding it becomes very hard to disguises units. Actually you don't even need UI modding, just the point of view about micro, UI and mechanics which comes with it. How do you infiltrate an opponent's army without them being able to notice it in principal?