I don’t think it’s just “being 3D”. Mario 64 put a lot of R&D into particulars of how jumping should work, the camera should work, and what the player’s goals should be. Quite a few games unintentionally copied them, while you could see some games not following their lead early in the 3D days that felt very janky to play. Tomb Raider could arguably be among them with the tank controls, though of course it has its own more niche appeal.
Legend of Zelda OoT followed up with popularizing a targeting button (good ol' Z-targeting) to focus on one object or enemy in a 3D space and move around it or fight/otherwise interact with it. Such targeting has been a standard feature of 3D action-adventure games ever since.
And it's a bad one if it applies at all. PC shooters of the time always kinda tried, but it didn't work. The original Half Life got dinged a few points in original reviews because of a few janky platforming sections.