I had the same debate when I was looking for a kayak two years ago.
Dishing out anywhere from $150 to $500 + bucks for a kayak is no small investment. I went with a SOT and am so glad i did. The ability to move more freely and even spread legs out a bit (in the water) is awesome. I got a Patomac from Dick's ($225 - was suppose to be $400 - fully loaded but... ) and its the best investment i made. Also the SOT i have is very stable and if there was ever a tip I don't have to worry about the yak filling with water an trying to turn it again. Also it feels more natural to be on top rather than in a hole. I can even stand on mine if i elect to do so in order to scout beds and weeds.
Good luck in decision.
I am actually going to create an article on my site
www.ezangler.com about the considerations of SOT or sit in for freshwater fishing. By the time i launch it would be great to hear what you opted on.
EZ Angler.
Last edited by ezangler on Sun Mar 17, 2013 3:33 pm; edited 2 times in total