What puzzles me is that the only difference between 'farming' AE missions and story based missions is that the story based ones were put together by people who took the trouble to add a little bit of text to the events in their farming mission. Seriously, that's all it takes. I played one of the highly rated farms that's on live: it was filled with interesting custom critters, pigs, ducks, and chickens. All it wants is a bit more text to become an amusing environment.
Since the missions I had published on live all died, I've put in a couple old favorites. One is 'Spread My Legions', a three mission story, villain oriented, in which you must assist Romulus Augustus to conquer the Past, Present, and Future. I ran this one when I needed tickets. The other is 'Who is Kidnapping the World's Great Philosophers', a one map story in which you must liberate philosophers and defeat Ayn Rand; it was meant as an allegory about the issues surrounding Wentworth's and the loss of value of inf. Both of these could be farmed if wanted; most are made out of recolored and renamed standard mobs, with the more annoying kinds excised, and a few custom characters. Both are story oriented. Both are farmable.