What are you going to use it for camping, long day trips, or just short trips solo or occasional tandem paddles? More for leisure or for getting in shape and a little fun workout?
I find Kayaks use more core strength and are better for a work out since you twist your torso paddling. Canoe's can be more leisurely, usually can hold more stuff, and just more versatile IMO. I generally find canoe's more comfortable for long outings. Kayaks seem to be more specialized depending on what you get. I am a little biased towards a Canoe but that is just me. I am not against kayaks but would want to try a few out before settling. Both can be fitted and accessorized according to usage and budget.
How you are going to haul it and launch it is almost as important to what you are going to use it for. The older I get I like the more expensive lighter ones. Its mostly a personal use and preference thing because there are many options out there.