Just have it go by number of men trained for the turns it takes. IE, playing on huge it'd be like this. Say you have 4 units of 120 men Hastati, so they each need 40 men to bring them back up to full strength, so 160 total. Since thats the same as normal unit, they get trained in one turn. But if you had 5 120 men Hastati units it'd take 2 turns and so on.

That might be too annoying to add in, so perhaps just a sit limit for each unit size level. 40-80-120-160(as maximum number of re-trained men per turn). Retraining shouldn't stop you from training a normal unit though as the two could go hand in hand and it might hurt the AI more then it helps to balance things.