Well I don't have experience with very many types of kayaks but I can tell you what I do know. You'll get what you pay for but for the novice or newbie who doesn't know where to start, here's a few pointers.
I prefer the sit in as opposed the the sit on because I fish and paddle cold water too. My family bought mine on sale for $400 reg $500 for Fathers Day. It came with a rod holder and small anchor. Equally important is the paddle which most kayaks don't come with. I don't like many of the collapsible ones but a two piece is better than a four piece and i like a long paddle. Many cheap paddles are shorter. I don't like the cupped paddles either. It's better if there is no wrong way to hold it.
Fishing kayaks have a flatter bottom for stability and white water kayaks are more rounded for speed and handling. I have no use for the splash skirt as it impedes my access to fishing equipment. If you are sitting in a kayak you should be able to easily access your tackle and a small container of bait.
I have a 9 foot kayak and it weighs 40 pounds. I have seen much longer that handle well and move with little effort but they'll never get back in the creeks where I do. I find myself doing the limbo under fallen trees and paddling over half sunken brush so compact is better for me. If I spent more time in the Great Lakes I would prefer the bigger model. Compact also transports on a car top easier. I have a short box pick up and can load all four of our kayaks in the back.
014 by wildniagara, on Flickr
You can buy kayaks with a rudder which makes fishing and trolling much easier but if your going to be in shallow water you'll want a retractable rudder $$$. Some come with a small compartment to mount the fish finder and if you want to pay up you can purchase a complete package. My sons yak had a built in rod holder which consisted of a molded plastic hole that holds the rod straight up. This proved far inferior to an adjustable Scotty flush mount rod holder. Some have molded rod holders behind the seat but I've never tried these but they seem inconvenient because you have to reach behind yourself.
The handles shouldn't drag in the water like mine. My Old Town kayak has a constant trickling of water as my handles troll behind me everywhere I go. My Field and Stream however has the handles on top while paddling and this also prevents my hooks from getting tangled in them when fighting a fish. The F&S does not track straight though and sucks to fish in because as soon as you stop paddling you start to turn.
For me I prefer flat with a large open hole to sit in but with fairly shallow sides so my arms don't rub while paddling. 40 pounds is a nice loading weight and 9 feet is ideal. I only weigh 155 pounds so my yak may not be good for heavier anglers. It's plastic and getting thinner ever time I beach it. I've already got 4 years and my monies worth for sure. I miss my tinner and Evenrude but I wouldn't trade my kayak for anything.
048 by wildniagara, on Flickr