If the only incentive to play content is for its narrative (and I'm not dismissing that as a valuable incentive, it is, just bear with me), and not for any reward/character development/game mechanics reason, then it indicates that there is a dissonance between the game design and the narrative. The two should be working neatly in tandem, but in CoH I believe that they don't. Where CoH is a game that encourages multiple playthroughs, but the content is underplayed, that to me indicates a colossal design issue (one which I think has existed in the game more or less from the start, gradually getting worse).
Again, I don't think that AE/Farming is the root of the issue here, but it does play a role in making the rewards obsolete. As biostem pointed out, a lot of the stories are inconvenient and irritating anyway, so replayability may be laborious for other reasons too.