Lot of good recs here. The big thing is to know what type of water you'll be doing the bulk of your fishing on. I made the mistake of buying the wrong yak the first time, but I made it work for me for as long as I could.
My first yak was an Emotion Glide 10'. Definitely a flat water boat, though it has some failings even there. It's not as stable as its design would lead you to believe, and balancing weight on it is more of a trick than it should be. I bought it with no frills or extras, and added all my rod holders after I brought it home. I had it fairly well rigged (2 flush mount rod holders behind the seat, and a surface mount up front), but it still lacked a few items.
My primary fishing style is downriver floating on a river with lots of class I & II rapids. Nothing big or dangerous (though, in the right conditions there are a couple of possible class III's). This yak was not meant for that at all. It's a flat water boat, and really lacks the maneuverability and stability needed for anything technical. I've spent years forcing this boat to bend to my will and run rougher, faster water. The final decision to go ahead and get a yak more suited to what I need came this spring when I flipped coming through a nasty little rapid that I've successfully run dozens of time with no issues.
So, the search began. I knew I needed a yak that would easily lend itself to being a fishing rig, yet handle the challenges of river fishing, as well as be a solid, safe and fun rig for the times when I just want to paddle fast, rough water for fun. I landed on two hybrid models from LiquidLogic: The remix XP10 (sit inside, almost pure whitewater boat, slightly modified to have some speed on flatwater with a deployable skeg for tracking) and the coupe ( a sit on top version of the Remix XP). I almost went with the Remix, but I quickly realized that my visions of running class IV and V's were just delusions, and that I really wasn't up to that challenge right now (maybe in a couple years, I'll add one to hte fleet and get real ballsy).
Once I had it narrowed down to the coupe as the most logical choice, I started searching for a used one. Not so easy. No one wants to get rid of them if they have one. I just happened to luck into a place in Salisbury, MD while visiting the in laws at Christmas that had a used coupe on display. For $550, it came home with me that day.
I haven't had the coupe out on the water yet. Buying a new yak in the dead of winter in West Virginia is pure self torture. This does give me time to tinker with it a bit. Test out what gear I can and can't carry etc. The coupe has a good amount of storage, so for the overnight trips, I should be able to carry my camping gear without being overloaded.
Since the Taco is a new addition, I really haven't put much into making it more friendly to hauling my yak. But, with a 10' boat, it's pretty convenient to just toss it in the bed, strap it down and go. The plan is to add a camper shell with racks and make use of J cradles since I usually have 2-3 boats to haul on most trips. I basically want to recreate the set up I had on my '02 Tundra Access cab.
Once I get more organized, I'll post some pics of the old rig and the new.
TThe point is, once I started fishing from a kayak, there was no other option for me. It's been the best thing I've done in years.