You definitely want a sit on top style kayak, the sit on top is more comfortable for fishing and it also allows water that you take on to drain away so you can fish in rough conditions without worrying about sinking. Then you just need to make sure you get a kayak that has good stability and decide if you want manual power or some sort of drive system. If you are trolling deep water I would highly recommend some sort of drive system as it is very difficult to troll deep water rigs without one. The drive system can either be a built in manual system or an electric trolling motor, both have their benefits.
I hear that sit on is better quite often. Now I have never fished off of one, but i have a 10ft sit in kayak and if you manage your gear correctly it is more than fine, and quite a bit cheaper. Costco has kayaks every spring for $325 (400 reg. with a 75 off coupon that comes around early april) that come with the yak, a paddle, a spray skirt (which i have never used, actually sold it on kijiji for $25) and a roof carry kit. All you need is to spend a bit of money for rod holders and it will get you into the sport. Between the yak and the holders and whatnot, I spent about $500 but I put in 2 flush mount holders, one cannon rod holder, 2 cleats, bought a small anchor and made a diy trolley for it. The kayak there (pelican quest 100 if you want to google it) is really stable, tracks well and has a couple dry hatches
I've fished the thames, the grand, maitland, the french and the bayfeild rivers and small lakes, went on st clair on calm days, and backcountry camped out of it almost a dozen times. Best investment I have ever made, hands down.