"To represent any point in a two dimensional space, you need two variables"
right?
For example (using our good old friend, The cartesian coordinates) we can talk about any point in two dimensional space using two variables, $x$ and $y$.
All fine and good!
Enter Polar coordinates.
Now this system uses the renowned $r$ and $\theta$ where theta is defined as the angle the vector makes with the x-axis.
AHA! "Angle made with the x-axis" so we need to define what the x-axis is? so does that mean we are using THREE things to talk about a point?
ps: My doubt can be extended for three dimensional spherical coordinates but lets keep it simple.
In polar coordinates, we're referencing a particle by its distance from the origin and angle relative to a reference point. There's no reason that reference must be the $x$ axis. It can be the $y$ axis or the direction of any other unit vector.