I guess the sitting part might be dependent on the individual. I personally have no problem being in my kayak for the entire day. In fact just this past Sunday myself and another Crappie.com member spent 11 hours in our kayaks fishing one of the local rivers and lakes. If you get the right seat, and have enough room to move your legs around, sitting for longer periods of time might not be a problem. The benefits of a kayak over a jon boat are numerous in my opinion. They are generally much lighter and easy for one person to handle. Kayaks are quieter for fishing the shallow waters. Kayaks are easier to paddle and go much faster than your typical jon boat that is being propelled by oars. And with the right kayak selection, you will be able to carry nearly as much gear as you would in the same equal length jon boat. Of course I have pretty much done nothing but fish from kayaks for the past 25+ years so I might be a bit partial.
It is not about the equipment you have to use,
It is about how you use the equipment you have. :D