Generally I don't care if the third option is there or not, but one place where “system” is useful is when the preference is in an app and saves to my profile. I usually use a light theme on desktop but dark on mobile. Though TBH if the toggle is in easy reach it is no hardship to flick it one way or the other.

A common gripe I have isn't the toggle, but that people often don't test both states, neglecting the one that they don't personally use, so elements creep in that are difficult (or even impossible) to read/see in one of the options because of contrast problems. If you are going to have both options, please test both options. Not having my preference is less annoying than being offered my preference but it not actually being usable.

As a side note, this is the ultimate light/dark mode implementation: https://tonsky.me/

Am I missing something? I get black text on a yellow background, and no apparent toggle...