After a year of rehabilitation to recover from Tommy John surgery, Jose Fernandez returned to Miami's rotation in 2015 and threw 64.2 innings. He battled a biceps strain towards the end of the season, but other than that, his return was a success. Entering 2016, the Fish have said that they are going to enforce an innings limit on their young star. While that may be a good idea for Fernandez's health in the long-term, it might not be in the team's best interests in the short term.
The Marlins have a fairly short window to contend. While Giancarlo Stanton, Christian Yelich, Dee Gordon and Wei-Yin Chen are all signed to long-term contracts, Chen can opt out after the 2017 season and Stanton's salary starts to sky-rocket in 2018, which will make adding additional talent harder for the thrifty Fish. Add into the mix the fact that Fernandez can depart via free agency after 2018, and the window for postseason success is most likely only two years wide. This means that Miami needs to do everything possible to win ASAP, and that means having Fernandez on the field.
This is where the situation becomes a dilemma. The Marlins need Fernandez to pitch deep into games on a regular basis to make the playoffs, but allowing him to do so could mean that he is unavailable to play in October. Joe Frisaro's article, to which there is a link in the first paragraph, suggests that the Marlins could limit Fernandez more during the early months to build up his arm for a postseason run. This makes sense as letting Jose Fernandez pitch away until he reaches 180 innings, and then shutting him down, could really hurt the team if they are in the hunt in September.
Perhaps, though, a pitch limit could be more effective. If Jose doesn't have his best stuff one game, then Don Mattingly could go to the 'pen after 80 pitches or so. Likewise, if the Fish build a big lead, Fernandez could be given some rest to preserve his arm for when the team really needs it. However, if Fernandez is putting up zeros in a close game, he needs to stay on the mound to give the team the best chance to win.
The 2016 season rests on Jose Fernandez's right arm. With the Cuban phenom on the mound, Miami has a good shot to beat anyone on any given day. It is sensible to protect his surgically-repaired elbow so that he can pitch at an elite level in 2017 and beyond, but the maintenance program shouldn't hinder the club's chances at competing this season. The Marlins are in win-now mode, and they need Fernandez to anchor the rotation all season long.
The Fish will possibly need more than 180 innings from their ace if they make it as far as the playoffs, so pitch limits and extra rest during lopsided games will help alleviate the stress on his elbow. Jose Fernandez is Miami's rotation. Without him, the team's starting corps are average at best. The Marlins need to make sure that they use him effectively and efficiently in order to succeed this year, and that directly relates to his workload down the stretch.