Sit-on top kayaks are fine for fun, family-type recreation where you're just cruising on the water. But any serious kayaker will tell you that spray skirts are the way to do, whether you're doing river or sea kayaking.

The biggest pro of sit-on-top kayaks is that they're easy to get on and off. Again, this makes it preferred if you're paddling around with a group or family where "everyone wants a turn."

But there are far more cons. For one, your center of gravity is going to be much higher if you're paddling a sit-on-top model, and thus, you'll be more unstable (and likely to capsize). Part of the nice thing about sit-in kayaks (with spray skirts) is that you're sitting really low on the water--lower than any other type of boat or canoe. Plus, with a spray skirt, you can do things like rolls that are physically impossible on sit-on-top models. Furthermore, kayaks with spray skirts can handle a lot rougher water.

Really, it's a question of what you intend to do in the kayak. If you want it for anything more than very basic fun, there's really no advantage to sit-on-top that I've found. Go for a river kayak with the spray skirt.