There are quite a lot of differences. The main one being that Ex2K integrates seamlessly with Active Directory, whereas you need to add a connector to 5.5 to get it to talk to AD. If you have 2000 servers on an NT.4 domain then go for 5.5, but if you have, or are planning to have Active Directory then go for 2000. Whilst it took me a while to get used to 2000 after administering 5.5 for 2 years, I really like 2000 now.
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