Here are my thoughts on kayak fishing, having owned everything from a $300 wally world special, to a $500 perception (both sit-in), to the $2300 Hobie Outback (12' with pedals).
Pros: quiet, peaceful, gives you some exercise, almost a more primitive way to fish, can get stupid skinny (but only with the pedals out), cool way to get into tournament fishing if you don't have a $$ tournament rig, can be a low cost way to get on the water. You don't have to pay for gas or maintenance and most people have a way to store it. You can obviously catch some dandy fish off of the things and be very quiet as a one-man operation.
Cons: You're always fishing by yourself, unless you go out in a little plastic flotilla, which can get annoying. It's actually less convenient than fishing out of a power boat, in my opinion, especially if you're car topping. For example; in my skiff, I back down the ramp, launch, park, and go. With a kayak, you unload the boat, pedals, seat, rods, crate or tackle bag/box, paddle, stick anchor or other (maybe both), fish ruler, cooler, etc. Then you drag or roll down the ramp, watching for boaters. If you car top, you're trying to control at least 80lbs up and down off your roof rack. Pickup beds are easier, and you can keep a lot more gear on the kayak during transport.
Pedal kayaks have way too much stuff for fly line to get caught on, so if that's how you fish, you'd have to use a basket or something.
There's no really good way to troll an area while standing, although while seated you can fish an area and keep moving at a perfect trolling speed. You're committed to fishing a relatively smaller area, closer to where you launch than with a skiff.
Lastly, you can't bring a girl on your fishing kayak.
PS. If you peddle a kayak you're selling it.
