To me I thought it was, since I was a 3:1 dog in the hand, the pot was laying me 2:1 and that I can also win at least a bet the size of the pot on the flop if he folds to my all in check raise.

It's pretty obvious Omaha isnt my number 1 game, so can you please comment for me?

(hand converter not working)

Table 'Tea' Seat #1 is the button
Seat 1: Villain($284.60 in chips)
Seat 2: xxxx($41 in chips)
Seat 3: xxxx($94.65 in chips)
Seat 4: xxxx($36.50 in chips)
Seat 6: xxxx($40 in chips)
Seat 7: xxxx($61.70 in chips)
Seat 8: xxxx($96 in chips)
Seat 9: stunnersuh ($116.25 in chips)
xxxx: posts small blind $0.50
xxxx: posts big blind $1
xxxx: posts big blind $1
*** HOLE CARDS ***
Dealt to stunnersuh [6d 3d 5d 6c]
xxxx: raises $1 to $2
xxxx: calls $1
xxxx: calls $2
xxxx: calls $2
stunnersuh: calls $2
Villain: raises $13.50 to $15.50
xxxx: folds
xxxx: folds
xxxx: folds
xxxx: folds
xxxx: folds
xxxx: folds
stunnersuh: calls $13.50
*** FLOP *** [3s 5h Jd]
stunnersuh: checks
Villain: bets $38.50
stunnersuh: raises $62.25 to $100.75 and is all-in
Villain: calls $62.25
*** TURN *** [3s 5h Jd]
*** RIVER *** [3s 5h Jd 2h]
*** SHOW DOWN ***
stunnersuh: shows [6d 3d 5d 6c] (two pair, Fives and Threes)
Villain: mucks hand
stunnersuh collected $239 from pot
*** SUMMARY ***
Total pot $242 | Rake $3
Board [3s 5h Jd 2h Kd]
Seat 1: Villain(button) mucked [6s Ad As 3h]
Seat 9: stunnersuh showed [6d 3d 5d 6c] and won ($239) with two pair, Fives and Threes

Terrible call pre-flop. You're not going to hit a flop that nicely enough to get the implied odds. You have to be pretty certain he has AA, so your only chance is hitting the set or two pair on the flop. If you're not ahead by the flop there go your implied odds.

And you did, you hit a great flop. But never play this again.

I agree that you shouldn't be playing this hand preflop, even for a limp. Even if you put the guy solidly on AAxx, you don't know his side cards and even if its just a naked AA, bottom 2 pair isn't a great situation to be in although probably +EV at this point. However, there are too few flops you can catch to justify calling that much preflop.

Ok understandable.
My thinking just was, this is a real easy hand to play, you either hit 2 pair, a set or some kind of big draw on the flop and can win a monster pot, or when the flop hits you simply throw it away.

Maybe I'm thinking too much in Hold 'Em terms? Like I was pretty sure he was sticking the raise with aces, and me "knowing" that he gave his hand away to me, that if I am able to hit a flop to that, he will have no idea where he is in the hand on the flop. If an A flops I can simply check-fold, if I hit a hand, then I can win at least a pot sized bet.

Still incorrect thinking??

All in on the flop is pretty straightforward I think. Very hard to put him on a hand beating two pair given his preflop raise. Mind you, if he has a jack in hand or AA (likely) and calls your raise, you need to understand you're not a big favourite at al (60:40 usually, round that region). Thus calling off an eighth of your stack preflop is not very smart, really. You will only hit two pair or a set a little over an eighth of the time, and on those occasions (combined) you'll probably only win his stack 60-70% of the time, so the implied odds aren't really good enough. Stacks need to both be about 250-odd BBs before you can consider this call, I think, and you need to have a good read on your opponent and position.