Here is a response I wrote on another board for someone that was also interested in fishing yaks....
If I can offer up some advice here, and feel free to do with it as you please. I currently own three kayaks, one sea 16' Sun sea Kayak, a 12' Wilderness Systems (tarpon 120) sit on-top kayak (that I outfitted for fishing, primary one) and a 12' sit in Inuvik kayak by Clearwater Designs (also designed for fishing) in Prince Edward County. All of these kayaks share one thing in common, they are all rotomould kayaks and fantastic designs. The nice thing here is that they can take a beating, and should you happen to put a hole in it, it's relatively easy to fix.
Given that you will be fishing out of it, and if you are like me, I can easily spend a whole day in the yak on the water, comfort is of utmost importance. With my sit on (cottage on Adolphus reach and pretty much all fishing done there or in upper bay), on warm sunny and hot days, I am often sitting sideways, feet in the lake, one to cool and two to slow my drift, and find it very comfortable for fishing this way. In addition to this, you'll want a yak that is easy to paddle and tracks straight. Nothing worse than paddling a barn door that doesn't go where you want it to. If you can find a dealer that does water tests, even better. When I got the clearwater yak, they offered a test 'ride' - this is a yak designed for the open water. Cuts easily through the waves and can store you and good amount of gear reasonably well. The tarpon yak was bought from a dealer just north of Kingston, and they also offered trials on any of their products which was fantastic. Both of these yaks i found required very little effort to propel them forward. I could paddle with just my hands.
Another thing to consider is weight and where you are going to use it. Are you using in small bodies of water, big lakes, is there a launch close by, or do you have to carry it? If you have to carry any distance, you'll want to consider a cart which brings me to storage and accessorizing your yak. You'll want one that you can mount things to, because before you know it, you'll be adding tons of stuff to it...it happens- it's like lures, you've got a tacklebox full, but yet you buy one more and it may only get used once. Well your yak is like that....anchor, rod holders, fish finder, go pro mount, etc... So if you are screwing into it, you'll either want to make sure you can attach nuts if using bolts, or good screws and maybe an adhesive. One additional consideration is drainage- sit in are harder to drain than a sit on top and during the really hot summer months, a sit in can get pretty darn hot! Also, consider where you are getting in and out of it, along with mobility, current and future. Sit in's are a little more challenging to get in and out of and heaven forbid you turtle it! easier to get back on a sit on than into a sit in if you are in the middle of a lake.
There's lots to consider when buying a yak, and the best thing to do is to find a model that will suit your needs and can grow with you. That may mean saving a little more to get the one you want.
Hope this helps!