So many great games. But honestly, fairly easy choice for me.
While Mario 64 did a fantastic transition for platformers, at that point in time I didn't care for classic platformers...at all. Yeah, controls were good, but it wasn't until a few years later and Rayman 2: The Great Escape that I felt that 3D controls got actually really good...as in modern standard good.
What really got my attention always was another type of platforming - one that combines exploration and puzzle solving. And now it was in 3D.
I'm talking about Tomb Raider, of course. Sure, the controls were a bit weird, but very Prince of Persia, and suited for that acrobatics approach Core's TR games had. Fantastic level designs and sense of accomplishment once you figure out the level. Loved it then, love it today as much as then. Hopefully announced remasters won't change that, or at least give and option for original controls.