The big reason to play with Marathon is for use with the larger maps where you want units produced in your home cities to have half a chance to get to the war front before they expire.
In Civ4, it was not unusual for a unit to take 10-15 turns to get to the front lines on a huge map. Wars often lasted for dozens of turns (a dozen-turn war was short in Marathon/Huge). So if you want to experience an epic war where you're constantly reinforcing front line troops on a huge map, Marathon made sense.
In Civ5, since huge maps crash frequently, I'm stuck playing on standard/large. Epic fits pretty well to those map sizes, more so then marathon.