I've got friends who use jon boats, toons, canoes, yaks, and even one home made wooden canoe. We argue all the time about the different advantages and disadvantages of each. We fish 300 acre or less lakes, small rivers, big rivers, slow rivers, and up to class 3 rocky rivers. Currently I have a tandem canoe (OT Disco 158, solo canoe (OT Pack), and a SOT yak (Jackson Coosa). I am going to stick to boats that are stable enough for fishing. For example, whitewater yak may take on class 4 water but is impractical for fishing. Also, when I say most yaks have a low seating position, there are several models (like the Coosa) that have a very high and extremely comfortable seat. Point? There are always exceptions. Standability and stability are highly subjective and all types have models that have that capability so I won't discuss that.
Here is my opinion and all of it is worth about 2 cents! If you must throw tomatos, please get them out of a can!
SOT Kayaks (the current rage these days)
Advantages
Most can be remounted after a flipping even in deep water
Less likely to wrap around a rock after flipping in a rapid
Do not take on water during high waves or monsoon rains - great for salt water work
Speed - a little faster than a comparable canoe but much faster than a toon when you need to cover a mile or 2
Light weight - depending on model
Most models do not catch a lot of wind
Easy to transport due to ability to stack in a truck bed or trailor - light weight ones easy to car top
Most models are fast even with a headwind - what I want when it is whitecapping out there
Disadvantages
Most models have a low seat and can be hard on bad backs
Low seat means decreased ability to see down into the water
Less gear storage than canoes - only relevent on camping trips
Heavier than a Royalex or Kevlar canoe of similar length - my Pack weighs 33lbs while my Coosa is 60lb+ both are 12 ft+-
Canoes
Advantages
Higher seating position than a yak for better sight fishing and all day comfort. My butt is 11 inches higher than my feet in my Pack
Tons of storage space
Easy to modify
Extremely shallow draft - many SOT have "tunnel" hulls that sit an inch or so deeper
Light weight - I once picked up a kevlar 14 foot solo that was only 25lbs - A Royalex 15 ft canoe = 55lbs - 15 SOT will reach 70+
Transport - I have put up to 3 in one pickup - important for shuttling river trips with several pals - I have stacked 4 + 1 SOT on my trailor
Disadvantages
You flip and you are sunk. I have done it in shallow water but in deep, you have to swim it over to the bank. I have had to help pry one off a rock once.
Catch more wind than a SOT but not as bad as a toon. If your canoe is leveled out, it is very managable. If one side is up high, it will weather vane like crazy.
Toon
Advantages
Most models I have seen have extremely comfortable and high seating position. Fantastic comfort for all day fishing. Hands down best fishability
Stable as nothing else this side of a real boat
Most can handle big rapids. I know guys who shoot class 3+ that I must portage in my Pack
Quiet rubber tubes make little sound when hitting a rock
Disadvantages
Wind - I have seen toons not be able to go down a slow river due to 20mph+ winds
Transport - hard to get 2 large toons in a pickup - many guys have special trailors
Slow - I have done a paddle down 2 miles, fish a mile of shoals, and then paddle back up to the car in a canoe - no way in a toon
Not as much storage as a canoe
Summary:
I prefer my solo canoe due to it's sort of a jack of all trades.
I can fish about anything but really rough water on large lakes or salt.
It will never be as comfortable as a toon for all day fishing.
It will never be as fast as a SOT especially in a head wind.
But it can do it all well enough for a wide variety of water and weather conditions.
You really need a couple of each but I ain't got the storage space or the money!
There is no such thing as the perfect boat. They all are great for certain types and styles of fishing.
Good luck with your boat choice and I hope I haven't muddied the water up too much for you.
Pics of me and my frinds various boats...
Attachment 8685 Attachment 8684 Attachment 8686 edisto0005.jpg Attachment 8682