Between Zygarde and Heatran, I've got to go with Zygarde. The typing, bulk, stats, and basically infinite sets that changed the meta have to make it a titan of the meta. Though Heatran's reliability and consistent viability despite Lando and Zard being everywhere make it a close second.
Evaluating the entire USM metagame, it's Heatran. Evaluating the entire SM metagame, it's Toxapex. It's really hard to ignore either Heatran's sheer utility and wallbreaking throughout USM or the absolute stranglehold position Toxapex took in the SM metagame. So ultimately, it comes down to a tie between Heatran and Toxapex, though for the sake of a choice and decided by a coinflip, I am going for Toxapex.