doing it your self can save you money and allow you more flexibility, and sometimes more time at what you want to do.
minuses would include that if you are not back to the ship on time, the ship won't wait. also if you encounter problems or get lost, you are on your own.
We do about half and half. For somethings that you couldn't save much money on, we sometimes go ahead and do an excursion. for others, especially when we have been to the port before, we go ahead and take off on our own. It all depends on you, and how you can handle the stress of the 'unknown'...