Most personal fishing boats are equipped with an Outboard motor because the motor is easier to maintain and replace, when needed, and the motor can be lifted completely out of the water when fishing by shore or in shallow water.
Most Family Bowriders / Ski-Boats are equipped with an I/O with the outdrive positioned beneath the swim platform offering easier access back on to the boat when skiing/wakeboarding/tubing or swimming.
In general terms, I/O's are best suited for family "fun" boats. The weight of the motor is inside the hull offering a smoother quieter ride. I/O's are similar to automobile engines and can be larger than Outboard motors offering more torque and horsepower for watersports than would be available with an outboard.
Outboard's are best suited for "fishing" boats. Not only are they easier to maintain/replace, the fully integrated seal around the motor and lower unit protects the whole unit from the elements where the inboard is constantly exposed to water in the bilge.
To learn more about the difference between Inboards, I/O's and Outboards please see the following article in "Lake Boss" written by Nathan B. Link: http://thelakeboss.com/?p=233