A difficult decision or not?

Here's a situation I'm struggling with:

I'm dealt pocket Aces in LP and raise to be called by one villain in MP.
Flop shows a rainbow K, 6, 3 and the villain bets 2/3 of the pot into me.

What could he have?

• pocket kings? unlikely because he limped and just called a raise
• two pair? unlikely, I don't see him calling a raise with a K6 or 63 out of position.
• pocket 66 or pocket 33? these are possible hands that fit his pattern.
• a draw? he might have an open ended straight draw or a gutshot draw, but would he bet that?
• a bluff? possible, but that would be a very daring play

So, I'm basically thinking he probably has a set or there is a small chance he is bluffing.

I played this hand like a total donk (cause I was tilting) by calling his bets on all streets. I should have laid it down when he bet again on the turn.

Still, I'm wondering what the right play is here.

Folding on the flop was the correct play of course, but wouldn't this be extremely weak? If I start folding top pairs on the flop everytime I get bet into, I feel like like a sitting duck: just bet me and I'll fold.

Looking back on that hand, calling doesn't feel right either. Most likely, I'll be facing another bet on the turn and be in the same spot again, only for more money.

I'm now thinking I should have reraised him on the flop. If he 3bets or even goes all-in, I have an easier laydown, cause I doubt he would take a bluff this far. It would be lost money, but now I did loose even more on later streets. The alternative would be to just call and give up on the turn if the villain bets again.

I definately would like some feedback on this, so feel free to post your thoughts.