Pretty straight forward question. Since Akainu will definitely not stay Fleet Admiral forever and since a new WG will emerge in which not Tenryuubito, but the Kings of the world rule together, Marines will still exist and need a leader.
I personally think that Fujitora is the frontrunner to becoming the new Fleet Admiral after Akainu's defeat/death.
Koby's dream is to become an Admiral, not Fleet Admiral and him becoming one is already a miracle in itself, he won't be FA by EOS of the story.
What do you think, who'll be commanding the Navy in the future?