I have limited experience with kayaks, but have used one intensely a few times. I used a sit in and liked it a lot. The problem I had, was the one I used was a little small for me. It was a 10 footer, and at 6'-1", 200#, it was just a little tight.
My Son however, is quite the accomplished Yak fisherman. He has a fancy dancy, all decked out, sit on top, 11 foot kayak. He probably uses his 4-5 times a week, literally.
When he was looking to buy, he was talked into a SOT. After using it extensively though, he has admitted he wished he bought a roomy sit in. The SOT yaks are very wet and can be very cold in the spring and fall. Also, they do sit a little higher as Dave described.
My wife used an 11 foot, extra wide, (sorta tri-hulled), blow molded model and fell in love with it. It was very wide at probably 30-31 inches for stability. Not quite as fast as the long, narrow, round bottom boats, but in kayaks, thosed details are give and take. The long, narrow ones are sleek and fast, but don't turn as quickly, and can be a little tipsy, whereas the wider boats don't move as fast, but they are considerably more stable.
Hope that helps...
Jon