Like you, I usually play Villager as a troll character, usually in doubles with a partner Villager for the pocket tree kill setups. Mario is such a solid character in this game that the only time you would need a secondary is a matchup that gives you, the player, a hard time. Villager can be useful as a secondary when you really need to play defensively as that's probably his biggest strength, but he really struggles up close thanks to his rather laggy attacks, and he's only really useful against characters with unsafe approaches or neutral like DDD, something that Mario already has little trouble with.
TL;DR Villager can be a defensive secondary for Mario, but the Italian "plumber" is good enough on his own that he doesn't really need one.