The purpose of it is for the camera for motion capability and to indentify which controller it is
Personally, I don't find it that annoying in the most part. When I'm watching Netflix it can be slightly annoying since it is so very redundant, but when gaming I don't notice the colour (making it pointless for those capabilities)
The only time it is really annoying is when I'm watching Netflix on my laptop at the same time and the light reflects off the screen