I'm a avid kayak fisherman and I prefer a SOT, I have a sit in as well. The SOT's can be remounted in the water if you turtle, a sit in will have to drug to shore, dumped out and then you can get back in. I run rivers with class 2 as well as lakes with my Perception Caster 12.5(a cheap but well built SOT) with no issues. There are three different manufacturing processes for SOT's. Best=Roll Molded, Good=Blow Molded, Not so good=Two piece (top and bottom molded separately then glued together)
If you paddle in flat windy water, get a rudder installed, you will thank yourself. You need a yak with a soft seat in it that you can replace/upgrade. I'm in my perception for as long as 12 hours on some float trips and its very comfortable. Paddle length is another consideration to make. Your height, how high you sit in the yak, how wide the yak is are all important in paddle selection.
I suggest buying a good quality "used" kayak. Top brands IMHO in this order; Jackson, Moken, Wilderness System, Native, Perception. If you buy new, go to a kayak/canoe shop and not Dicks or the like. They will match you up for what you want to do, most price match and they will let you try out some demo's. I have shopped at Hook-Line-Paddle in Willmington and they are very knowledgeable and they will let you try out their yaks. They sell off their rental yaks at the end of every season so you may want too look into that as well.
If you have any more questions feel free to PM me here