The contrast. When a human is a villain in the MLP world, it's a big contrast to the usually harmonious pony society. Their different ways of thinking and acting can create really interesting storylines. For example, a human might be more driven by power or greed in a more 'human' way compared to the ponies.
Well, the new MLP comic could offer more detailed backgrounds and enhanced colors. Also, the plot might have some unexpected twists and turns to keep readers engaged. Plus, it could potentially have crossovers with other related franchises.
One idea could be a villain OC who has the power to manipulate dreams. They could enter the ponies' dreams and create nightmares, causing chaos and fear. This villain could be motivated by a desire for power over the dream realm.
Well, 'The Rogue Human' is quite popular. In this fanfic, the human villain has a complex backstory. He starts off as a normal person but due to certain events, turns into a villain. He has some really interesting interactions with the ponies in Equestria. Also, 'The Malevolent Man' is a fanfic that you might like. It portrays a very evil human character who is constantly devising plans to take over the pony world.
A corrupt politician could be the new villain. He uses his power and influence to cover up his illegal activities, like embezzling funds meant for the city's development. The Punisher would see through his lies and decide to take him down.
Adventure is also quite common. The new world of MLP New Generation offers a lot of scope for creating exciting adventures. Fanfictions may have the ponies exploring new lands, facing dangerous creatures, or solving mysteries. Additionally, the theme of acceptance is seen a lot. The ponies have to accept each other's differences, whether it's in their appearance or their abilities.
You can start by looking on fan - fiction websites like Archive of Our Own (AO3). There are often a lot of niche fan fictions there, and you might be able to find some great MLP New Vegas ones. Just use the search function and type in the relevant keywords.
Another interesting MLP New Vegas fan fiction idea could be that the main characters from New Vegas encounter a strange portal that leads them to the world of MLP. They are shocked by the colorful and magical world and have to learn how to interact with the ponies. Some might be skeptical at first, but as they get to know the ponies better, they realize the value of friendship and start to adapt to this new world.
Perhaps the new hero in the mlp fanfiction is an outcast pony. They don't fit in with the normal pony society at first. But then, a great danger looms over Equestria. A powerful force is sucking the magic out of the land. This new hero realizes that they have a hidden power within them that can combat this threat. They must then overcome their own insecurities and the doubts of others to save Equestria.