I also prefer a SOT (sit on top) vs. the sit in type. As mentioned before, easier self-rescue, no need to pump, etc. Also, much easier to shift your body around to get good casting angles. You can even sit sideways (like on a bench) with your feet in the water and drift. In a sit in, your body is more or less locked into a straight-forward position. Also, SOTs offer better areas to keep fish and store gear (on top and not inside the yak). Many mounting surfaces for extra rod holders, fishfinder/GPS, etc. I think most SOTs tend to be a bit heavier though.
SOTs are not as dry for the paddler, even if you use scupper plugs, compared to a sit-in with a spray skirt. However, dressed appropriately (I wear a farmer-john style wet suit, booties, and a Simms drytop) I fish comfortably in as low as 55 degree water (prime striper season) as long as there's some sunshine.
I have an Ocean Kayak 15 Prowler and it's a great boat. Tracks very straight even when paddling hard (i.e., no side to side bow shift). I probably could have gotten away with a 13 Prowler (I weigh about 185-190). But heavier guys like the 15. If you're going to do rivers, you may want to consider a shorter boat (easier to turn) or a rudder, but it won't be as fast or as stable in choppy waters.
Ocean Kayak and Wilderness Systems both make great boats.
Good luck!
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