The version that currently makes the most sense to me is this:
* Quaternions are a complete distraction and should be ignored. i, j, and k are (xy), (yz), (zx) bivector rotation operators (up to a factor of -i or something like that). Pauli matrices are the same and should also be ignored.
* The factors of "theta/2" in the exponents that are used in representations of rotations using quaternions (rotating vectors with e^(R θ/2) v e^(-R θ/2)) are distracting and should be ignored.
* The best way to see what is meant by "the space of rotations in SO(3) is not simply connected", you need to think about paths in _rotation_ space carefully. More carefully than I did as an undergrad! (Although I'm sure this is obvious to people who have studied the approach math in a course?)
The wrong approach -- which I was stuck on for years -- is to think about a point on a sphere in R^3 moving around. A vector that starts at, say, +z in R^3 and is rotated by 2pi in the xz plane ends up where it started exactly.
The key insight is that 'non-simply-connectedness' refers to _paths of rotations_, rather than paths of what the rotations act on. So imagine gradually rotating that vector +z in the (xz) plane. If you go around by 2pi, you've made a path that can be modeled as an exponential operation: e^(2pi (z^x)).
The question is: can this path be deformed to the identity path? It seems like it can -- you just change from rotating +z all the way around a great circle, to a smaller and smaller circular path until it is just rotating in place (and xy rotation). But somehow when you collapse it, you still have a 2pi rotation! It's just that now it's a 2pi rotation in xy rather than in zx. No matter what you do, if you collapse the rotation path to be the identity on the +z vector, the resulting path rotates _some_ vector by 2pi, instead of keeping it at the identity.
So in physics, it's not that there is a negative phase factor _per se_ that matters for physics. It's that there are two physically distinguishable states (identity rotations and anti-identity rotations) -- so two different electron wave functions can't be identified as the same electron, because they are a 2pi rotation apart just due to how they got there. And the fact that we _model_ this is as a negative sign is entirely an artifact of our obfuscating choices of mathematics for the situation.