This is definitely one of the things that I'm most excited about. I always felt like heresies in-game didn't get much attention other than "not-standard-religion". *Maybe* something distinctive here or there (Cathar with women, for example), but nothing really notable. For me it really just because a "free CB to attack anyone from my former religion" type of decision. Imagine having actual mechanics governing Catharism, for example, which not only believed in equality among the sexes but also an anti-greed, anti-wealth, anti-ownership culture. Imagine penalties for accumulating too much wealth or land, or bonuses from being poor (or from giving out money, etc).
Of course, for that type of intricate detail I'd almost imagine a DLC, but we'll have to wait and see.