I don't care if MS is getting better lately.

The fact it's getting better is obviously a positive thing, but will it stay that way in the future? no one knows.

I like the fact Github is independent of all the big players. I really, really, really hope it stays a neutral ground.

Also, if acquired by MS, I'm not that afraid for github itself. However, what is at risk in my opinion is all the integrations around github. There is a rich and striving ecosystem surrounding github. Tools like appveyor, travis-ci, coverall, readthedocs, codacy are really useful, ease a lot development and are infinitely easier to setup/maintain than a Jenkins box plus a few slaves. What would happen to this ecosystem remains to be seen.