The thing people don't know about 3D physics (and the games that rely on them) is that there aren't 3 axes. There are six. The X, Y, Z stuff is just linear positioning. You still have to account for angular positioning with Yaw, Pitch and Roll and learn how convert between them cleanly without a variety of mathematical and systems errors that are often hard to perceive, hard to fix and hard to plan for.

You need to understand geometric calculus just to implement basic 3D logic. When you have to worry about pathfinding and AI, that multiplies issues and when you add in multiplayer and all of quasi-temporal maths and logic problems that causes, the move to 3D is exponentially more complex than 2D.