Until the 2012 season, Flores played SS since being signed. I'm assuming he's a decent athlete.
Flores is a big kid and the Mets played him mostly at 3b last year, but he also got some games at 2b and 1b. Flores probably has a projected MLB ETA of 2014, so with the Mets unsure of Wright's future, putting him at third last year wasn't a bad move.
He's a big kid and although he could probably handle 2b for a few years, he'll probably outgrow the position. There was always talk that he would end up as a corner OFer, but he's not very fast.
This year will be interesting. If he remains at 3B, he'll likely be a trade chip. If the Mets intend to keep him, he'll obviously be moved to another position.