Main is the top screen, sub is the bottom screen. The naming convention stems back from the DS scene which had two video engines: the main engine (which can do 3D graphics and has more VRAM) and the sub engine; each screen is assigned 1 engine (can be either way around). But for the 3DS, main is always the top, and sub is always the bottom.
It is indeed possible to control both screens' backlight independently, but it is not a good idea to do this, because the 2DS only has a single screen. Controlling both ensures that it behaves the same on a 2DS and 3DS.
All operating systems have their flaws; but overall I choose to use Windows. If I had to use anything else, I'd use FreeBSD with GNOME 3 though; you should too if your main concern is stability.
Interesting that the 2ds just uses one screen... Never tried freeBSD but I do use GNOME 3, it's my favorite DE so far