100NL: OOP: 2pair when flush completes on river

Poker Room skin
No Limit Holdem Ring game
Blinds: $0.50/$1
10 players
Seat 1: BU ($42.25 in chips)
Seat 2: SB ($137.50 in chips)
Seat 3: BB ($20.00 in chips)
Seat 4: UTG ($122.80 in chips)
Seat 5: UTG+1 ($29.00 in chips)
Seat 6: UTG+2 [ JS,AS ] ($107.35 in chips)
Seat 7: MP1 ($32.80 in chips)
Seat 8: MP2 ($90.95 in chips)
Seat 9: CO+1 ($22.25 in chips)
Seat 10: CO ($97.00 in chips)
Converter

Pre-flop: (10 players) Hero is UTG+2 with J A
2 folds, Hero raises to $4, MP1 folds, MP2 calls, 5 folds.

Flop: 9 J A ($9.5, 2 players)
Hero bets $7, MP2 calls.

Turn: 4 ($23.5, 2 players)
Hero bets $15, MP2 calls.

River: 3 ($53.5, 2 players)
Hero bets $25, MP2 raises all-in $64.95, Hero ???

villain was 20/5/2. I had a ready that he raised sets on flop & turn.
With my read I was pretty certain he didn't had a set, he could only have a flush (unlikely as this was a back door flush), TP or 2 pair.
I've better 1/2 pot OOP to have calls from TP or 2 pair. He pushes, I'm getting 3.5 to 1 to call, I think this is a standard call, right? Would it be better to check-call to give opportunity for villain to bluff?

I don't think this villain has a backdoor draw too often, but that is just based on pf stats, so take that FWIW. I guess it could be Ahxh/QhTh, but that is about it.

If you check, AQ/AK could check behind as there is not a lot that they are beating and the board is getting pretty scary. A9 may still bet, but why give him the chance to check behind. Busted draws may or may not bet. With your read that he doesn't have a set, the call seems pretty straightforward.

this is a passive guy, so b/c and b/f should be considered in the first place.
his line did sound to me like a backdoor flush on the river. However, I'd have hard time folding my top two in this spot given that he might raise some worse two pairs and you put more than 1/2 of effective starting stack in already. cry and call, buddy.

Crying call

Thanks guys, yes I cried and called!