All are great fishing tools.
I like the Hobie Mirage and the Jackson FlexDrive pedal systems. I think the Mirage drive is quieter. I KNOW I can sneak up on fish with it. I haven't had the FD out enough times yet to determine how fish react to it yet. You can go in shallow water with the Mirage....just make short strokes with the pedals far apart.

If line management is a concern, maybe a paddle kayak is better because of fewer things to tangle the line on.
I think Drew Ross has owned both the Mayfly and the Coosa FD. He is/was on Jackson Kayak pro staff, I believe. He'll give you an honest review of both. And he flyfishes for grass carp!
Here's his blog, which also has links to his Facebook and Instagram.
http://looknfishy.blogspot.com/