I am certainly not an expert on this but here is what I have read and observed.
SOTs are often aimed at entry-level paddlers. They offer simple use (no spray skirt) and usually high initial stability. The stability is achieved using a relatively wide flat bottom. Thus they are very stable in flat water paddling. The compromise here is that they are less stable swells. To correct this problem a designer would have to raise the height of the sides of the kayak above the waterline. In order to keep it a SOT they would then have to raise the height of the seat. This would radically reduce the stability of the kayak. If the designer left the seat low between high sides he would end up with a cockpit without the benefit of a spray skirt.
Don’t get me wrong. Not all SOTs are relegated to entry-level use. Some advanced kayakers select them for their high initial stability. Fishermen for example like a stable platform to work from. Surfers like the hard edges offered by some SOTs. Racers use SOTs with very a narrow beam and a round bottom. These are great for speed but lousy of stability.
All that being said I would favor a cockpit model for general paddling. But if I found myself doing a lot of fishing or surfing, I might add a SOT to my list of wants.
Don 
: I would be interested in comments on Sit On Top kayaks vs. the Standard
: Cockpit that requires a skirt to prevent flooding in open water.
: Much of the danger in kayaking seems to revolve around the Standard Cockpit.
: Following a capsize, if the captain can't perform a successful roll, he or
: she is out of the boat in the water and the cockpit at least partially
: flooded. This exposes the captain to a wide variety of dangers. Getting
: back in is difficult without lots of practice in rescue techniques. Even
: when the captain is back aboard, there is the water to be gotten out and
: the skirt to be reattached, both difficult jobs in rough conditions. There
: are techniques and equipment for dealing with all of the above, but it
: seems like there are still a lot of places for things to go wrong.
: Magazines like Sea Kayaker are full of articles where conditions made it
: next to impossible to perform these techniques. The answer always seems to
: be "more practice"!
: Sit On Top (SOT) kayaks, on the other hand would SEEM to possibly have
: answers for much of the above. I have no experience, however, in actually
: using them. I would like to hear from anyone who has experience with SOT
: kayaks in the size and configuration of a standard sea kayak or
: 16'-20'surf ski. Questions I am pondering are: - What are the upsides and
: downsides of the SOT configuration?
: - What is the technique for getting back in if you come out in open water?
: Can you just climb back in?
: - Are these boats rolled or do you simply bail out and climb back in?
: - Do you end up sitting in a puddle of water all the time?
: - Is the lack of protection on the lower body an issue or do you just wear
: protective gear such as a wet suit?
: - Why is the SOT configuration so popular on surf skis? (Because they are
: easier to get back into?)
: I don't know the answer to these questions and am hoping some of you have
: experience and can steer me straight.
: Thanks!
