As I understand it, molecules form into shapes which space electron pairs so that they are as far apart from each other as possible. So, two elements bonded to a central atom form with a 180 degree difference between them, three form with 120 degrees. The part that confuses me is when there are four atoms around a central one.

 

In that case, a pyramid is formed. I visualize this like it is popping up off a 2D plane and into three dimensions. My question is, if it can so easily "pop" into three dimensions in order to space the electrons further, why can't it pop into higher dimensions? Is my visualization all wrong?

Its kind of hard to understand your question. What demensions do you mean by higher demensions than 3d?

Any of the others. Don't some theories support the existence of more complicated dimensions that are unobservable to us?

As I understand it, molecules form into shapes which space electron pairs so that they are as far apart from each other as possible. So, two elements bonded to a central atom form with a 180 degree difference between them, three form with 120 degrees. The part that confuses me is when there are four atoms around a central one.

What you say here only is true for molecules without free electron pairs. Free electron pairs (which are not involved in bonds), also count. That is why water has a bent structure as well.

 

In that case, a pyramid is formed. I visualize this like it is popping up off a 2D plane and into three dimensions. My question is, if it can so easily "pop" into three dimensions in order to space the electrons further, why can't it pop into higher dimensions? Is my visualization all wrong?

Your visualization is not wrong, but why would you expect it to go further in higher dimensions? It is for precisely the same reason that you cannot go through higher dimensions. You, me and all of us are 3D people and all matter around us exists in 3D, so the structuring of molecules also is confined to 3D.