Travis,
I will take a stab at this but Mid Tenn Kayak Angler can probably add more. In my opinion the maneuverability of the canoe will not be near as good as the kayak. The way that you paddle a kayak is better for fishing, plus the low profile to the water gives you advantages also. There are more options for tricking out kayaks although a lot of the stuff could be used on the canoe. The biggest advantage that i can think of is the speed of which you can paddle the kayak will be a lot faster than the canoe.
Last but not least a kayak just looks a cooler than a canoe.
Hope this helps some. I will be interested to see what others have to say on this subject also.
Roy
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