Darkness in anything is like Cinnamon: a spice you use just enough of to add some flavour to things.
Batman's a nice example. A relatively sedate, bouncy show without Tim Burton's gothic influence and you get the campy 'Brave and the Bold'. Add in a bit and you get 'The Animated Series'. Add a little more and you get the Nolan movies.
Go nuts, you end up with 'All-star Batman and Robin', a strange book that has a scene where Robin is kidnapped then expected to eat rats, for some reason.
MLP is mostly fun and joy. Adding darkness ended up with 'Part of One', The Royal Wedding' and 'Lesson Zero' where genuinely surprising elements appeared and have been beloved ever since.
But were talking about tiny amounts of darkness. They're there to give the plot enough teeth to hook you in, something MLP:FiM doesn't need to do all the time. It's got comedy and adventure in there too. Though, darkness can then highlight issues that the magic of friendship, rainbow lasers, potatos or whatever happens could then attempt to fix. It would be bland if everything was all good.
Just as Pinkie would be dull if it wasn't highlighted how dependant on others she is or how nerotic Twilight can be. Or that there are insectoid creatures hellbent on sucking the compasson from you like a walking juice box. Or that a slight tweak to the timeline would result in all out war.
I'm for a little spice in the show. Just not too much.'m not lookng to have a Darkness Challenge again so soon after watching 'Man of Steel'.