My understanding is that $\cos$ is defined by the value of $x$ as you trace the graph of a circle counterclockwise, starting at the point $(1, 0)$. Similarly, $\sin$ traces the $y$ value. I understand HOW the trigonometric functions work. The issue that has been gnawing at me for years is WHY they are defined that way. There's probably a totally reasonable explanation, I know the history of Trig goes back thousands of years, but I don't understand the reasoning behind defining the Trig functions with the most arbitrary, least intuitive possible rules.
If I had been the person to invent $\cos$ and $\sin$, I would have defined them by starting at the topmost point of a circle, and trace it clockwise. Is that not the most intuitive method? Maybe it's just a modern preference, but it seems to me that we humans like to read things left-to-right, and yet the trig functions are defined starting from a circle's right-most point. Furthermore, $\cos$ and $\sin$ start at $x = 1$ on a circle's graph. Why not start at $x = 0$?
I think this is why so many people have no intuitive understanding of $\sin$ and $\cos$, and why many students get through high school and college by simple rote memorization of what a handful of $x$ values evaluate to in $\sin$ or $\cos$.


I have no insight on historical issues, but my understanding is: precisely because we read left-to-right.
This is how the abscissa axis was born, horizontal and left-to-right. Then the ordinate axis had to be vertical, positive from the ground up to the sky.
As the X axis has precedence over Y (it was born first), nothing is more natural than counting positive angles from positive X to positive Y.