With the new crew focus system, the marines act as an additional "subsystem". The marines are effectively locked into being set as "marines", and don't help with any of the tasks on the ship.
For one thing, I don't believe this is historically accurate. Marines would have helped with manning the guns and handling lines. But let's ignore that for now.
The purpose of the marines is to help with boarding combat. Shouldn't they at least help with the "boarding" subsystem? If I switch on "boarding", a bunch of my non-marine, able seamen leave what they're doing (guns, sail handling, etc) to go and prepare for boarding. The whole reason I turned some of my crew into marines is so that they would help me in boarding combat, so why aren't they included in the number of crew that's getting ready for boarding combat?