First except the fact that there is no one size fits all boat and work backwards from there. You might want to consider accumulating a few boats for different applications, but that brings the problems too, of more money, more maintenace, and storage.
Personaly I use my two man canoe for most of my applications (light enough to move easily and easily maneuverale in the water). My 14 foot aluminum car top with a 9.9 outboard for bigger water. I also have a bellyboat for times when space is an issue. I would say the belly is the worst. (work to get into, and alot of work to move long distances in the water). Future boats to add to my collection will be a WaterMaster Raft for floating streams and small rivers, a 20 foot river boat with a prop and a jet out board on the back the jet for the shallows and the prop to save on fuel when I don't have to use the jet, and lastly a floatplane to get to out of the way places without abusing my vehicles.
Now here's another thought over the last three years I have been shying away from boats in favour of fishing where I can fish from shore or by wading; less work! Doing the watercraft thing means a longer day, when you consider loading at home, loading at the water, unloading when you come off the water, unloading when you get home, and cleanup; something to think about.
My advice: If I were to start from scratch today I would be looking into one of Canoe Man's Flyers, or one of his Canoes. Since Canoe Man and Son fish regularly they know what us anglers need in a watercraft and have made all their equipment with that in mind.