Losing to a higher set is definitely one of this game's most annoying tricks. If he was in one of the blinds and checked to the flop, you could easily put him on two pair, but against a good player, like you said, 99 can be a limping hand. Having a lower pocket pair against an opponent is always a recipe for playing a hand uphill. I guess you just admit that he played the hand well and beat you, and just move on.