When switching from Windows, it was very confusing to me, that program files where all over the place. It was before (almost) every distro switched to the /usr directory, so it was even worse than it is now. Even now, when I understand more about Linux than before, I still prefer the Windows way.

I think that this hierarchy is nice for people moving from Windows, but experienced enough that they could understand the docs and tweak the OS.

I was actually surprised that this distro was designed with more experienced people in mind, I thought it was for beginners.