These are totally different OS kernals, aren't they? Isn't Win 2000 the first one to run without DOS while Win 98 is completely DOS based? Win 98 is FAT32 & Win 2000 is NTFS. Moving from 98 to 2000 in NOT an upgrade ... it's a complete install. Pretty bad comparison, really. Nice stretch, but that's like me saying I moved from RedHat to Suse and it was tuff.
At least you were able to move from 98 to 2000. Try that with 2 different versions of Linux.
Point is even windows service packs have broken applications. We are on an nt4 domain which I used to use the domain management tools right off the DC, when I went to SP they no longer worked. I also had to wait a good long while before third party apps like cygwin worked on XPsp2.
US I run three different versions of Linux on the same box! I have changed from one to the other all the time, its really not all that hard.