The kid just turned 21. He's coming off his first season above A+ ball, and his first where he has shown signs of hitting for power.
I think the Mets have two options:
(1) Allow Flores a full season in AA ball at his corner position and see where his trade value stands after 2013. The fact that he's the Mets #1 positional player (recent trade not included) doesn't say much -- his trade value is low -- prior to 2012 he only touched double digit HR's one time and most of those weren't even in A+ ball.
If 2013 is a successful campaign and his slugging and OPS prove consistent... then his trade value will increase.
(2) Move Flores to the outfield as the Mets infield appears blocked for the foreseeable future. The only position that remotely exists is 2b... but there seems to be a logjam of sorts. The reports say his feet are too slow to play OF, that his first step isn't quick enough. The kid played SS in 2011, a position which is typically filled by the top athletes on the diamond.
The obvious downside to the position change is the potential for a decrease in offensive productivity, which is his best quality and may further lessen his trade value.
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Given those two options, I go with #1. It takes an exceptional athlete to change positions and be productive. There are those that have done it, but I would venture to guess the list of failures far exceeds the list of successes. Give him a full season in AA and if he succeeds he should be dealt for organizational needs in the offseason.