That would be due to the fact that OS X ran on non-Intel for quite some time. Only as of 2006 did it run on Intel and with it came the ability to also install Windows next to OS X via Boot Camp. Back then Apple wasn't very popular but this has changed over the years due to the iPod, iPhone and iPad. It's these small things that let to the current situation where people are looking at a Mac when buying a new computer. And because of that people are also starting to compare it to other brands and thus to Windows.
I don't think so. A lot of people didn't like Yosemite and a lot won't like El Capitan either. With the 3D effects back in El Capitan, albeit subtle, I could live with it if I had to. I suspect however that as others venture outside of Apple as I did recently, regardless of whether they like the new looks of Yosemite, I think they'll find most Linux, BSD, and Windows versions even worse looking. There was one version of Linux that looked sort of interesting and its name escapes me, but it's still Linux, which to me isn't a selling point any longer (been stung by Linux more than once in my life).