Honestly, the problem with the Zelda series is that the story-telling hasn't evolved since... Well, since the NES days, if you think about it (or at least the OoT/MM days).
I mean, it's implied that the Hyruleans committed genocide against the Shiekah but nobody gives a shit.
Granted, I think Ganon is (objectively) bad (I've only just started TOTK) but honestly? He at least becomes more introspective and less violent by the beginning of Wind Waker, at least, meaning that he's capable of evolving to at least some degree.