Best hitter: Christian Yelich
There are some organizations that have so many talented hitters that trying to single one out is tough. The Marlins system isn't one of those. In fact, after Yelich, the most talented hitter would be Kyle Skipworth, who hit a combined .208 during his first two seasons before finally upping his average to .245 last year.
Yelich does have plenty of promise, however. He offers plenty of potential to hit for high average (a la Mark Grace or Will Clark), as well as some decent potential for power, but there are plenty of scouts and fact-checkers who aren't sold on his ability.
Regardless, check out the video and you'll find that Yelich has one of the prettiest, smoothest swings in all of the minors.
Best pitcher: Chad James
James was one of the most highly-regarded high school pitchers coming out of the 2009 draft. Taken by the Marlins 16th overall, James has had little success since signing. He posted a 5-10 record in 2010, complete with a 5.12 ERA and nearly 5.5 walks per nine innings. He racked up 18 wild pitches and while James was very stingy with the home runs (only three allowed all season), he still didn't have the kind of debut the Marlins envisioned.
In Yelich and James, the Marlins have two very interesting, high-ceiling prospects who could both turn out incredibly well. However, both players are still way too young to try to make any call on how good they could be. Both need to get back onto the field and prove themselves worthy of their first round status.