Remember I'm a classic gamer here people.
I would say the biggest advance would be Zelda OoT after Link To The Past. Link To The Past was so small and confined. Then OoT comes out, and it's enormous. Especially the dungeons. And there are so many tricks and hidden treats you can find through out the game. It was the first one with a horse you can ride, it introduced gold skulltulas, gorons, gerudos, friendly zoras, and a whole cast of new items. And above all else it introduced THAT MOTHERFUCKING OWL. Damn you Shigeru Miyamoto!