Very interesting HH. Your line screams set as much as a line ever could (limp preflop, call raise, c/r on uncoordinated flop). There are only three/four hands that villian could possibly have that justify his call. (This assumes that you haven't been playing hyper aggressively recently, nor has he.) AA/99/AKs/AQs (possibly a 44 who is willing to get stacked in a set over set). Given the way the hand played out the only hand he could have that would justify a call (but not push) both flop and turn is ATs (where s = spades).

I don't think I could fold Axs (spades) on the flop even to an obvious set, but perhaps I should. I think you played it fine.

The problem with 2 pair is any lead is tenuous and so many cards become scare cards.