I prefer a sit on top for fishing for the following reasons.
1) It is easier to get in an out for wading. In winter I wear neoprene waders or dry pants, but I still wade and stay warm.
2) It is easier to get in and out when landing or launching.
3) In rough conditions, water comes right in and drains right out - no bailing or pumping needed
4) The increased leg mobility is much more comfortable.
5) I can put both feet out to the side in the water to add stability.
6) It is easy to sit side saddle to fish when I am drifting slowly. Sometimes I do this with swim fins to control my drift.
7) it is easy to turn around and face completely backwards to fiddle with rods and gear completely behind me.
8) Self Rescues are easier.
9) Assisted rescues are easier.
10) Less gear is needed. I don't need a pump or a bailer or a skirt or a cockpit cover. I have less need for a paddle float depending on the boat.
I'd love to hear from others what they prefer and why.