"easy call for me...you're only down to 3 hands in villain's range, and nothing really indicates that he has one of those 3."
Limped in merely called raise preflop in position, that doesn't sound like a medium pair to you? At the very least the man called that with a suited ace and now has two pair.
Not really that bad of a way to play it. He knows the OP isn't afraid of the ace, he bet out on the flop with the ace showing. Based on the pre-flop action, it's safe to say a good ace. If he just smooth calls the flop bet, OP will now get suspicious and may not put anymore money in the pot. So, he tries to give the impression that he's weak and trying to steal the pot by moving in knowing there are few hands that would call him, namely AK, AQ or a set and he is only in bad shape to the aces. Villian is either stacking OP or only getting his bet on the flop, this is his only chance to get more than the flop bet.