Oh my Princess Celestia, yes.
This sounds like an awesome idea, but I do wonder how possible it would be to mix it with feudal Europe. For one thing, there's three distinct types of Ponies (without even counting in the possibility of Griffons, Zebra and Buffalo); does CK2 even have any possible way to do racial traits, let alone how to deal with armies with mixed-races? Any quadruped army should move much, much faster than an all-human army, while Pegasus Pony-and-griffon armies should move stupidly swiftly and basically ignore all terrain except oceans - to say nothing of the fact that, since Pegasi control weather, and Unicorns have the power of magic, they should pretty much dominate any human army they fight, up to and including the potential for an all-Pegasus army of comparable size to just route a human army without taking casualties with thunderbolts whilst flying far higher than any archers can shoot, to say nothing of the effects they could have during a siege, both as defenders (good luck getting your bowstrings and catapults to work in non-stop torrential downpour, let alone actually trying to assault the castle through a field of muck,) and attackers (non-stop rain and lightning-strikes will have a pretty deleterious effect on the morale of defending garrisons.)
And that's just one pony type, albiet the one with the most consistently warfare-applicable powers. Individual, exceptional unicorns can be much, much more dangerous on the scale of warefare than a pegasus pony army, but most non-exceptional unicorns will be much less effective, if for no other reasons than that, being ground-bound, they're within range of human archery and foot/mounted attacks.
I love the idea, but until the game is capable of handling such distinction, I don't see it working out too well. Plus, I imagine Ponies would probably have to count as more than one human for purposes of supply (they're large quadrupeds, they need more to eat.) I'm not sure the game is, at-present, moddable enough to really take into account the kind of magic that Equstrian ponies are capable of, or even the simple fact that an all-Pegasus Pony army could fly across all of Europe in like, two months and would be very, very hard for humans to even hope to hurt - they can literally wage war by just sitting on top of clouds and kick lightning and rain out of them, so the only times they'd be remotely at risk is when they land on the ground to eat. Short of getting the Wizard Merlin to lend out, mortal humanity would be literally helpless against this kind of warfare. It may not be a very efficient way to kill, but it would certainly be devastating to morale.
This is all, of course, to say nothing of the impossibility of a human army laying siege to a cloud city. The only way they could hurt them would be indirectly, by attacking the Earth Ponies who provide them with food.....
I'm starting to see why in the past, the Pegasus Ponies were the warrior culture.