If I'm hopping between the 2 parks, I'll often do a hybrid.
From MGM I'll take the boat to one of the resorts, then walk to the park.
From Epcot, I'll walk to either the Yacht Club or Swalphin and then catch the boat from there.
The Biggest time sink in the boat ride from park to park is the resort stops. Since the resorts aren't that far from the EPCOT entrance, I basically bypass some of the stops and walk that stretch. That way I still get a bit of time off my feet, and can still easily beat the boat to EPCOT.