I think folks get hung up on which boat is best. Really it's about matching the boat to what you need, and getting it to fit into a budget
For myself, I love jon boats. They are flatbottom strong little boats. The flat bottom makes them very steady in the water when standing up or moving around. They also get on plane at lower speeds with less power, and can hold more weight. They are great for flyfishing from, and when combined with a jet make for a very handy little boat. Keep in mind they are only this good when made wide enough and with a decent thickness of metal.
they draw backs are when waves are encountered, if you have a flat nose boat they really don't like any real waves, so you can opt. for a modified hull, which has a slight v to the front. Still they tend to slap waves of any real size.
For myself I run a little 1436 jon boat that putt's me around just fine. I can do about 32Mph on the river with 2 nromal sized guys in it, and I can take waves in around the 3ft mark, I have done bigger, but really shouldn't be done.