If you can commandeer the ship and take it to where you like, it would be neat, but I suspect it would be a lot of coding work for the devs. Thus, my guess is that it's just a scripted event.
If, however, the devs did let you take your own boat back and forth, it could be very neat. You could go to the various port cities, sail around towards high rock, go towards morrowind and vardenfell (maybe even blacklight - wouldn't that be neat), go up river to windhelm, perhaps go up river past solitude and make your way towards (or close to) morthal. Perhaps there is more than one place to dock or land on Solstheim - even a beach will do if you're headed to the northern parts of the island. And maybe you can sail up solstheim's rivers.
However, once you've done all that, there needs to be something more to keep you entertained on your boat ride - maybe pirate fights, sea monsters and such.
But these are all musings. I suspect it'll just be a simple scripted event.