As Bruce implies, that's so broad a question as to be inappropriate in a
tech newsgroup. You should do some reading.
However, in my opinion the most important differences are reliability
and device support. Reliability because W2k, unlike W98, is much more
than a pretty mask over a DOS structure; it is a fundamentally different
architecture designed to prevent common system crashes and other
misbehavior. Device support because it is a newer and much more powerful
system. It is also easily set to resemble any W98 appearance you prefer.