As Konami's worldwide technology director, Merceron supervised the production of the FOX Engine, the in-house game engine that powers Metal Gear Solid V, P.T., and Pro Evolution Soccer.
No official word has been presented from Konami as to why Merceron has left, though many speculate that it's due to Konami emphasis on mobile gaming (and pachinko machines, really) moving forward. Others believe that he may have been snagged by Hideo Kojima for whatever project he's churning in the background. Or it could just be that he has been let go as standard practice once a project as grand as MGSV has been finished.
As far as I'm concerned, Kojima can announce pretty much any video game project he wants and it would garner nigh-unprecedented levels of fan support and crowdfunding, if he chooses to go that route. I wouldn't surprised if we hear that Merceron has joined forces with Kojima in the near future, or that other developers at Konami tied to its console IPs depart as well.