Microsoft still owns the majority (90%+) of the desktop market and the office market. They always had kind of crappy mobile os and that hasn't changed.

Sure but the smartphone space at the time was an insignificant percentage of the market. That's by far no longer the case now. Having a crappy mobile OS in 2000 is a magnitudes smaller problem than having a crappy mobile OS in 2016.

Is there any reason to believe that Apple would have follow led the way to mobile/phone/tablet if it were acquired by Microsoft a long time ago?