I have yet to fish from a kayak, but like you, I am seriously interested. I have been scouring Craigslist for deal on any one of the more reputable angling kayaks like the OK Big Game and Trident 15, the Wilderness Systems Tarpon 160i, and Malibu Kayak X-Factor. I think the fly line snagging issue has a lot to do with kayak design (e.g., foot pedals, rudder cable locations, etc.) and how you rig the kayak. For flyfishing, I would assume less is more when it comes to adding things like rod holders, depth finder, etc...basically fewer things to snag fly line. I have been lurking around
www.norcalkayakanglers.com for information on kayaks and fishing opportunities. The folks on the forum mostly fish conventional gear for fresh and saltwater. However, I am sure there a few members who fly fish from a kayak. It might be worthwile to drop a post for tips on kayaks that are flyfishing friendly.