Villain was fairly loose aggressive thus far. He was 3-betting a lot of my raises when I was massive chipleader on the bubble.
In this particular hand, I decided to flat because villain called a lot of my 3-bets in position then played ultra-aggressive OTF. Would a 3-bet/fold been better?
Folding pre seems like a wise choice to me for the reasons that the others have stated. Continue with a nice stack and equity in this SNG, look to return the favor to your opponents by making steal raises when you have the button.
As played, what makes this hand awkward on the flop is your stack depth in relation to the pot. Calling the flop is the best way to counteract this awkwardness.
A6 is just one of those hands though where you won't often win a big pot but can often lose one. I'd rather just fold it and call hands that have less of that possibility about them.