With MCA: Reborn the villagers are just so dynamic I guess, you can set them up with chores, chat/flirt with them, have them follow you or help you fight. Plus MCA has village building, a bossfight with the grim reaper to revive deceased villagers, outlaws and infections.
I mean if you combine the dynamic aspect of MCA with the villagers of Pixelmon, you can have villagers "party up" with you so you can take on raids or do double battles. Or you could even request pokemon battles with them, or make outlaws "attack you" with pokemon. Make it so villagers can direct you towards gyms or some sort of landmark by ASKING, or request trades or "help them" manage their pokemon for said party system.
Now yes you would probably have remove stuff like the graveyard system, infections and the grim reaper or at most replace it. But I would think it would be so cool to build a village and have travelers come in and out of your town through an inn, making trade for pokedollars after setting a pokemart, or requesting duels if you set up a battle arena. Or party up and help train a couple of villagers (or family) pokemons to make their pokemon as good as yours or even better to take on REALLY difficult raids.