In all fairness fairies aren't just cute little sprites that dress themselves with flower petals. Fairy also applies to elves, changelings, and also supernatural folk that were not only dangerous to humans but could tame animals and control plants to an extent, though that's heavily dependent on the type of fairy. Some of them may be cute but others are anything but, and the type's weakness to steel is parallel to their traditional weakness in folklore; wrought iron.
Problem is Game Freak decided to go with cute Pokemon to be Fairy types... and as for Light typed Pokemon... what are they supposed to go on there? There's not a lot of light beings in the world; at least concerning fairies they have a lot of folklore to work with. The only thing that directly correlates with light are angels and the like, and you'd only end up with one or two Light typed Pokemon that also happened to be legendaries.
But going with the main theme of a more mature game... why not involve a war? X and Y's lore mainly centered on a war 3,000 years ago that brought a lot of death and destruction, and there's not a lot of things much more horrifying and hellish than a war. As for mechanics, I can see certain evolutions evolving because of hatred, but not the absorbing poison bit. If you get bit and poisoned it doesn't spread to your party members; they'd have to suck the poison out to even get a chance at being poisoned, and even then it's rare. Having your Pokemon die because they were fainted too long isn't entirely realistic either because your Pokemon aren't actually unconscious; they're just not strong enough to fight in battles. If they were you couldn't fly or surf around on a fainted Pokemon or use any HM moves while said Pokemon was fainted, and they couldn't be revived via Rare Candy. But there are instances of Pokemon dying in the series, so a plotline death isn't entirely impossible.
And finally as a last note, Pokemon is already a pretty dark series. We have two games focusing on turning Pokemon into soulless killing machines, five games focused on the end of the world, and one villain who's stated goal was mass genocide. That's very dark, and that's not even taking into account that there are beings in the Pokemon universe that can pull you into different dimensions, suck your life away, put you in unending sleep filled with nightmares and erase you from the time/space continuum, and even the lesser Pokemon are fully capable of killing you. There's plenty of darkness there; it just hasn't been fully shown yet.