Sit on - all the way. A good stable sit-on will allow you to stand when you want. That's essential for flipping into cover, fly fishing, and other tactics. All kayaks designed expressly for fishing are sit-ons, to the best of my knowledge.
The apex of that pile is the Hobie Pro Angler, but there are other kinds if you don't mind using a paddle when you could be holding a rod. I wanted a kayak exclusively for fishing, and after a lot of research bought a PA-14. No regrets at all.
Canoe Pack Liner
Kayak Deck Gear Bags
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