Perhaps this will help in geometrically identifying the extra parameter. Two pure-state qubits are related by a unitary that spins the Bloch sphere about some axis by some angle. To specify that unitary, one needs three parameters, even though the location of each state is specified by two parameters. The extra parameter in the unitary is there because there is a whole family of different unitaries that will take the first state to the second one.
How can we interpret this redundancy? Let's think about the family of unitaries $U(\theta,\mathbf{n})$ that rotate a Bloch sphere by angle $\theta$ about axis $\mathbf{n}$ such that $U(\theta,\mathbf{n})|\psi\rangle=|\phi\rangle$ for a pair of states $|\psi\rangle$ and $|\phi\rangle$. If $\mathbf{n}$ pointed to the north pole, the two states $|\psi\rangle$ and $|\phi\rangle$ would have to lie on the same lattitude (polar angle); for example, two states on the equator could be transformed into each other. One can always change their viewpoint of any coordinate system to pretend $\mathbf{n}$ points to the north pole, so this picture will always be valid. The question now becomes: given a pair of states $|\psi\rangle$ and $|\phi\rangle$, what possible rotation axes $\mathbf{n}$ will allow the two to be connected; i.e., what are the axes for which $|\psi\rangle$ and $|\phi\rangle$ are at the same polar angle?
The answer comes directly from symmetry: given two points on the Bloch sphere, find the shortest path between them; i.e., the great circle that connects the two, which is unique. Take the point halfway between the two points and draw the perpendicular great circle. You can visualize this as orienting the coordinate system such that one point is $\varphi$ degrees above the equator and the other $\varphi$ degrees below the equator. Then this perpendicular great circle, like the equator in the visualized coordinate system, defines the set of rotation axes $\mathbf{n}$ that can connect $|\psi\rangle$ and $|\phi\rangle$.
The magic is done! We have reduced the two parameters of the unitary $\mathbf{n}$ to a single parameter specifying a coordinate on the "perpendicular great circle." Once that is specified, there is only one possible rotation angle $\theta$, so the problem is complete. We see directly that the redundancy in the unitary is caused by choosing which point on the perpendicular great circle to choose as the rotation axis. Of course, these transformations are only the same in that they all enact $U|\psi\rangle=|\phi\rangle$ by construction, but they are different unitaries in general and will not all perform the same action on some other state.