Good discussion guys, I guess it really does come down to one's preference. Linux, does a really good job of breathing new life into older machines that is for sure. And, it pretty much rules when it comes to SoC. But, But...
I think hermine makes some good points about windows. Probably, the reason why I still prefer it over Linux for my arcade. Let's be fair, winXP and win7 are both rock solid when it comes to stability and compatibly. Keep in mind, that WinXP is based on the NT kernel which has its roots in UNIX. On the other hand, I'm starting to loath win10 the more I dig into it. So, I still prefer winXPsp3 or win 7 over it.
Here are some other pros about windows that might start a friendly flame war with the Linux enthusiasts. Like hermine pointed out, windows still has broader support for emulators and drivers. I would even argue that MAME still runs better on windows, less input lag than say SDL on Linux. Maybe, SDL2 is better but I haven't done any real testing to verify that.
So, I still give windows the advantage for now, but this could all change in the near future. And, thanks to retroarch for bringing more emulator comparability to Linux and Android.