I am not really sure about the slowness of em/disembarking. The issue is really about how considerate are we towards one another. From my observations in various locations, the most time delays are caused by selfishness and antisocial behaviour rather then any other causes. The berthing of the boats and em/disembarking of passengers is no doubt slightly longer than that of an MRT train, but seriouly speaking, how much additional time do you think can we save? There should be staggered timings so that in case someone misses the bus or train, they can always catch a boat.
The bigger issue is to improve the public transport conditions and providing alternatives to the monopoly of the 'state' controlled transport companies.