Usually, I choose the "good" way with characters, some might say it's boring but I like it, and anyway that's not the question here : in fact I wondered if the "good" way really was good.. Let me explain : if you go through with the good main quest, then you will help neutralize the side effect of the energy-T ( more or less, I oversimplify to avoid spoilers ) and help bring peace in Ancaria. Therefore, you contribute to unite the different nations in Ancaria, and by doing so might accelerate the time when Lumen should come back,( since he left and said he would only come back once all Ancaria is united). And speeding things up to the point where we are under the dominion of an entity is far from good wouldn't you say? And in the other han, the bad main quest grants you powers beyond imagination, maybe enough to end god's dominion over all kind and bring back free will ?
So what would you say is really the good and the bad side here? ( if we elude the inquisition's torture and all these stuff, and we just talk about the big picture )