Things to consider
I have had my yak (Tarpon 140) for about a year and with work and all, have been able to go ouut abouut a dozen times. Here's what I have found from fly fishing in this thing. Keep in mind that I am in Oahu and mainly use it to transit the flats.
1. Lower point of view. As long as you're quiet in your paddling, you'll generally be within 10 feet of fish before you see them. Have your rod at the ready with some line stripped out. I have my stripping basket up on the bow by my feet.
2. Time to troll. Some spots take a while to get to. Might as well troll something behind you (plug on a spinning rod).
3. Wait about 6-9 months after you buy your yak before you put stuff on it. The fewer holes in you yak, the better. Do yourself a favor and get some of the bungees with plastic hooks (K-Mart sells these in the automotive dept). These things are invaluable in use (sticking a rod/extra paddle under the tensioned line).
4. If you're paddling around areas with shallow rocks or coral, buy one of those small paddles (aluminum pole, hard black plastic blade). I spent too much on my good paddle to use it to push myself off coral heads, un-beach myself, ding on something hard.
5. Buy a rubberized anchor. These things scoot fairly fast when you're not in them. I don't want to be THAT GUY that chases his yak across a flat.
6. Rudders...up to you. I like mine, but then again, it is a rudder system that isn't the recommended one from Wilderness Systems.
7. I like having an open tank well in the stern vice a dry-storage compartment (think old WS Tarpon 160). Easier access to some stuff I bring, like the cooler. It also serves as the seat for my 6-year old when he comes out with me.
7. You mentioned casting. Sometimes, I remove the back-rest and sit in the area just aft of the actual seat. Line is coiled in the seat portion and when I see a fish, I'm able to straddle the yak, make a cast and end up scaring the bonefish anyway. I'm working on it, but I've only done this method twice since returning.
Just as with anything, it takes a few times to learn the hows, whats, and what not to do's.
Listen to your kids after you ask them what they did today.