Prior to Mario 64, 3D gaming was broken as fuck. Many developers were fruitlessly trying to adapt a 2D gaming formula into 3D - linear stage design, play through the level, get to the goal, advance to the next stage. It was a mess of shit.
Nintendo fundamentally changed the way these games are designed.
Nintendo gave Mario 64 a hub area, with the levels accessible from this hub. The idea is that the player would play these levels multiple times with different objectives.
The design of this is ingenious:
1) levels are non-linear in design, creating a sand box environment to explore rather than a series to obstacles to navigate. i.e. Nintendo automatically made 3D gaming fun and engaging right off the fucking bat.
2) having a small number of levels which get replayed multiple times allowed the developers to spend more time on making them memorable environments.
3) player progression through the game is locked behind the number of objectives completed in other levels. This allows the difficulty of the game to be dependent on the player's skill level. Need 10 stars to unlock the next world? You only have 9? Can't beat that tricky level? Don't worry try one of the easier ones and as you get better you can come back and try again. Genius.
4) player exploration is encouraged and incentivised and the player is conditioned to marry 3D spatial awareness with their skill set. That ledge up there looks interesting but its too high to jump to? If only you could master the triple-jump or jump off that wall to reach higher.
5) having different objectives in each level allows the play style to constantly change, remain refreshing and always surprising. You never know what you might have to deal with next time you play that level.
And I haven't even mentioned things like the controllable camera or analogue controls.
The simple fact is that the gaming landscape can be split into BEFORE Mario 64 and AFTER Mario 64.
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