I have been thinking about a pedal kayak (Hobie or Native Watercraft) for my fly fishing. I basically am tired of alternate paddling and casting as I am blown around Midwestern lakes. Using my feet to hold the boat is place sound like a great alternative. My concern is the flyline being constantly entangled in the pedal mechanism. There is always lots of loose line underfoot when fly fishing. It is one thing to dump it onto my feet in a canoe, but another to get it near those pedals. Does anyone have any experience?
I flyfish from a Revolution…
that said, I do not flyfish and pedal at the same time. The coordination to do that would be insane, especially given the need to operate the rudder. 
Simple answer, the pedals will not be much of a problem for your flyline, everything else will be however.
I usually sit side saddle when flyfishing, (Dangling legs over the side) and strip the line into the water, which takes some practice to strip to the side.
I would get a small anchor for the kayak, and use it to prevent the drift… May need two to use one for and one aft, with a Anchor Pulley system.
FY
Fly line
I use a small collapsible stripping basket that goes on my waist to keep the fly line off my pedals. I’ve heard of some guys using a towel overs the pedals but I like to keep them useable and it seems a hassle.