I have two big positional prospects in my minor league system both of which will fill positional needs of mine in the (hopefully) near future. One of them is a poor fielding second baseman that I will eventually move to play in the outfield  Hardball Dynasty – Fantasy Baseball Sim Games - Player Profile: Melky Peguero and the other is a very recently drafted shortstop that I'll end up playing third because of a need there:  Hardball Dynasty – Fantasy Baseball Sim Games - Player Profile: Clarence Boyle.

I'm in the free agent signing period and wondering if I should be signing a long-term (three years+) deal for third base or LF/RF? Right now I'm thinking they both need one more season of development although Peguero is still very young and might need a bit longer.

Any advice?

Both of them need a lot more development.  3-4 years should do it.

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A lot depends on your team and your other options.   It wouldn't hurt either of them to spend a couple more seasons in the minors.   Peguero is much closer to BL ready, and could play in the bigs now, while we can't really tell about Boyle as he has no development pattern.   But Boyle at 3B within the next couple of seasons, barring insane development, is a losing proposition.