I looked at what castes of ponies have, and normal ones look pretty balanced. EPs are very useful for industry. Tough maybe give them increased healing rate in addition to strength and stamina, and some natural skills, like swimming. PPs are fast, and therefore great for hauling and scouting and hunting. They are also pretty good for 'going outside' jobs, because their dodge can keep them alive while they run from danger. Their flying, even broken, is still somewhat useful as long as there is a path, that a non flier could follow. UPs are great for industry too, and have an extra grip. I'd rather train them in crafts, than throw them into combat tough.
If something is imbalanced, it is 'abnormal' ponies. An army of spider ponies is pretty unstoppable, and some castes have 2 gripping horns or tusks.
BTW is there a built-in way to make only Princesses nobles, or are they treated like anypony else?
If there is a way to manipulate gender rates, I've read somewhere that they are around 2/3 females.