I am addicted to kayak fishing at this point. But keep in mind that I have caught tons of fish from the kayak this week. I am on cloud 9 after a great day yesterday and a good day today.
Anyway, I used to find fly casting from a yak to be a bit of a challenge. But I started in a very old whitewater kayak with a small cockpit. When I bought a new yak (both sit in kayaks not sit on tops) with a bigger cockpit I was much better off. The bottom of the boat (between my knees) is my new stripping basket. Line tangles are not an issue.
And I fully agree that you can get very close to fish in the yak without spooking them. So I leave the He-Man casts at home and rely on shorter casts with a focus on fly turn-over and fly placement (close to rocks etc).
And when in the yak you can get close to some pretty rocky areas that larger boats cannot touch. This can be handy when fishing for stripers.
I also really rely on my paddle clips. Having a place to stash your paddle is a plus. When the paddle is secured to the side of the boat you do not have to worry about it. Oh and buy a paddle leash. If you ever let go of your paddle and it falls over the side while you are fighting a fish then you will be happy that you have one. I made a great leash out of one of those plastic golf balls with holes in it and some nylon cord.
Ditto on the success of trolling the fly. I caught a nice striper this morning on the troll just before sunrise on a gummy minnow. After catching that fish I cast to some rocks nearby and caught a few more fish as well.
And finally, I do have some experience fly fishing in a major river here in NH (mouth of the Piscataqua). While fly fishing in very strong current while in the yak is not ideal I will say that this river is pretty wild and wooly yet there are areas of swirling eddy like current that offer some relief for the yak bound angler. When in these eddy areas my kayak really does not drift and I can still drop a fly into the raging rips and do the deep swing that can produce some decent fish here in the NE salt.
One last thing: if you are physically hauling the yak long distances when getting it to the water or to your car, especially across pavement, then forking over the $60 - $100 for a 2 wheeled kayak carrier (bungees onto one end of your yak) can save you a lot of effort.
I used to simply use the yak to access remote sand bars and such. But when the fish are schooled up and busting bait I love fishing from my little plastic kayak.