I'm taking this question as 'the most revolutionary upgrade to 3D for each series', or like which game had the biggest impact, and I voted for Mario.
Prime was a huge risk changing the genre to fps but it worked brilliantly. Though since it came out some years after fps games had already become popular on consoles, I feel it made less of a historical impact, even thought it is very different from standard fps fare.
Ocarina of Time was revolutionary because it was really the first 3D adventure game on a grand scale and set the bar for the genre forever after. But Mario 64 set the bar for 3D games in general. It is still a blast to play today and it's still fun to even just run around in circles and jump around in the game. I'd say Zelda and Mario are close but I give Mario 64 the edge.
Anyway, there's a bunch of different ways to take this question, but that's my take on it.