Other than the fact it came out after Win2kpro, not a lot really.
A lot of people seem to rate 98se above it but I thought it was no worse. It needs slightly more power, but enthusiasts had systems capable of running it just fine. No ability to boot into DOS, not ideal but by that time most people didn't need to run DOS mode applications. Finally there were a few driver issues with certain hardware but in my experience this was typically due to software refusing to install due to not detecting Win9x rather than necessarily a flaw in the OS itself.
What really annoyed me however was that I seem to be the only person that wanted to call it WindMill, not Me
I think the real problem MS had is that win2kpro came out a good 6 months beforehand and piracy was on the rise as more and more people were getting online. So people would get hold of Win2kpro (which was pretty damn expensive if you wanted it for home use) via dubious means and then obviously by comparison WindMill wasn't much cop.