Look at the kayaks gathered at any put in and you'll see plenty of similarities between each boat, but none of them will be exactly the same.
Unlike bass boats which are all laid out mostly the same between anglers, kayaks are known to breed customization. With the ability to drill into the plastic deck, any flat surface can become a rod mount, a camera pole, an anchor trolley, or, that perfect spot for a sticker.
Learn how to setup your fishing kayak based on the way you fly fish, and the species you target, and you'll be closer to landing more fish. Once you can vision the entire layout of your boat in your mind, the kayak becomes an extension of you.
The kayak performance you need for your local fishery
It's easy to pick out a boat because it's just the one you saw first, a friend's boat, or a feature in a video series, but before you make a purchase, ask what level of performance you need. A kayak is different from a motorboat, as the hull design dictates how fast you'll go, how well you can turn and how enjoyable it will be to travel long distances.
If you're fishing in big water with a need for those long paddles, pick up a longer boat, 15 feet or above. If you need a turn-on-a-dime-river-runner, get a short boat, ten feet or less. If you're fishing in the surf, get a sit on top, but if you're only fishing flatwater, a sit inside will work well. If you need something fast to battle heavy tides, aim for a slimmer boat that will cut through the currents.
A place for all of your gear and gear in all the right places
When kayak fishing first started, anglers were forced to customize their gear storage needs on their own in the garage. Milk crates were the standard tackle container, and pool noodles wrapped around every rod (still a pretty good idea). Now you can find a boat with the storage and capacity to fit your needs.
I've always been a minimalist, as in one rod, one box of flies in my seat back pouch, and any tools attached to my PFD. That's it. You may need a boat with a capacity of 500 pounds to carry all of the rods you need, but I recommend carrying as little as possible. The same goes for rigging. The more accessories you bolt to your kayak's deck, the more you will snag your fly line and ruin a cast. A heavier kayak is also a slower kayak, and sometimes you need to paddle quick to hit the fish.
Check your needs against your current experience level (and budget)
You may look at your fishery's conditions and decide you need the slimmest, sleekest kayak to which you can attach rod holders. Hold on. Are you used to paddling a boat with a loose primary stability, which means it feels "tippy" with any movement? Checking your current skill level will make sure you don't buy a boat you can hardly paddle. Being comfortable on the water is more important than catching fish, because when you're comfortable you have more energy to focus on things other than staying dry.
Your budget is also important. I've longed stared at beautiful wooden sea kayaks with a glint in my eye, but as a fishing writer, that's just pure fiction at this point. Kayaks that perform at a pro level, the ones that are light enough to lift with a finger and outpace a seal with every stroke, will also have a cost that makes the experts dizzy. If you're just starting out, buy the boat that suits your needs enough to be comfortable on the water, and comfortable explaining the cost to your spouse.
Do you want to paddle or do you prefer to pedal?
When it comes to paddle or pedal boats, I have a bias. I only use paddle boats, because I love paddling. Also, I've spent too much time untangling fly line in the gears of pedal boats to have my fill.
I have friends that love fly fishing from their pedal kayaks, and if you need to travel long distances, or just prefer to use your legs over your arms, then by all means pick a pedal boat. I'd never steer anyone away from pedals. I'd simply show them the graceful style of a perfect sculling draw stroke, and then ask them to do the same with their feet.
Get your kayak ready and tweak as you need
While you could spend years customizing your boat, endlessly tweaking it to perfection, it helps to know where to start. It helps to look at the kayaks at your local put in for ideas, but the way you fish and species you target will dictate your needs. Setup your kayak for your style of fly fishing, and start getting more fish in the boat.
Learn more skills and tactics for catching fish from a kayak in my recent book, Kayak Fly Fishing: Everything You Need to Know to Start Catching Fish.