I can think of a couple reasons: 1) weight - two stroke is much lighter and this can be important in smaller boats. 2) price - in my case check out a 75hp Yamaha 2-stroke versus an 80 hp 4-stroke.

Again, in my case I'm considering a 2-stroke main 75hp motor with a 4-stroke kicker. Reason being that, typically the main motor is used hard for 15 minutes, shut down and then the kicker is used for 2 hours. Fire up the main motor for 30 minutes and then use the kicker for 2 hours...... For my fishing, a 4-stroke kicker is a must. Make sense?