MamaMuto

He-he-hey, man. So from what I read in your post, it seems like this story would have a strong connection to the past (which I'm assuming would set up why the world is how its described in your little blurb.) Since it seems like the new ponies have a moderate connection to the old mane 6, why not double down on that concept and give that same sort of generational connection to the villains? For instance, think of the changelings. The world you've described looks like it'd be filled with despair; Chrysalis and her changelings cannot feed on despair. I don't know what your headcanon is for the changelings' society and life cycle, but let's just say the drones live 30-50 years and the queen lives for 200. Since they're changelings, one would expect them to adapt to their environment faster than most other creatures. So the five-hundred years pass, and the changelings have...well...changed. They no longer feed on love; fear sustains them instead. They thrive on the uncertainty and dread that the crapsack world you describe generates. This gives them a reason to oppose your protagonists who, I'm assuming, want to restore Equestria to its "golden age." This generation of changelings have physical similarities to their ancestors, but everything else is so different. Their M.O., their methods of feeding, etc. all different. Chrysalis probably wouldn't recognize them as her descendants. They'd seem vaguely familiar, yet so different and just...wrong. If you decide to take this route, that's the feeling I think you should want to evoke from your villains. I know I really only gave you one idea for a villain, but I feel like it's much better to give a formula for many more potential characters. I'm about to go to bed, but if you message me later today, I'd be happy to brainstorm some more ideas with you; it's my favorite part of the creative process. Hope you were able to gain something from this.