At this point, if Discord couldn't beat them by making them act opposite of their Elements, then there's only one real way to beat them: Go for Twilight first. Discord had the right idea of "divide and conquer", but the fact that he went for the others first instead of Twilight just was his downfall, as was not directly dealing with Princess Celestia in the first place (he had Twilight on the ropes, but because of his failure to deal with Celestia like Nightmare Moon did, she had time to save Twilight, who saved the others, and he grew cocky).
Anyways, for hopes for villains, I still don't see why they haven't went with the whole "Get six ponies who represent the opposite of the Elements of Harmony to battle our heroines" approach or even an alternate negative universe where the Elements of Harmony of the Equestria we know are feared supervillains in the Negative Equestria. As cliche as both of them are, I seee with good writing it would work.
Yeah... you could tell I've run out of ideas for a G-rated rogues gallery for this series. Give me permission to submit borderline psychotic characters into the canon, you'll get a military mastermind who sees the only way to stop Twilight and her friends is to just plain execute them (kind of like that cult in Past Sins, except with less Nightmare Moon worship and more "down with god princesses, up with a REAL dictator").
from dark to chaos six ponies will fight the fight kindness laughter generousity loyalty honest and magic makes it all complete the elements of harmony controlled and tamed to fight the fight to win the war against chaos and disaster
tell me what you think i made it up for this thing