Copied from initial commission request, because he said it better than I can:
"My idea is that while the Elements of Harmony stripped Luna of Nightmare Moon’s influence—whether possession, an adopted persona, or a super-powered evil side I don’t know, and it’s really not important—they didn’t re-write her personality, meaning that she still has to deal with the emotions that led her to becoming Nightmare Moon in the first place. Living in a new time, new culture, and among new ponies would just make it harder.

I imagine that she spent a good many nights alone, struggling with her fear, anger, and jealousy, wondering why she’s still feeling these emotions that she doesn’t want, desperately trying not to fall back into the same traps all over again, paralyzed because she’s afraid to go to someone for help but at the same time knows she needs it, and terrified of herself because she doesn’t know which side is going to win out in the end."