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The primary issues with running Exchange 2000 on a domain controller are resources, disaster recovery and security. Both Exchange 2000 and Active Directory are resource-intensive applications. This means that the memory, CPU and other hardware resources in the system need to be powerful enough to handle both of them together, especially under stress.
The second main issue is recovery. In the event of a disaster, it's going to take you much longer to restore if you have to first recover AD before you can restore Exchange. On a non-DC server, recovery of Exchange is much easier and faster.
Finally, there are security issues to deal with. If your Exchange and AD admins are in separate teams or groups, the AD team might not want Exchange administrators being authoritative on their DCs, and the Exchange administrators might not want the AD folks to be authoritative on their Exchange servers. Note that some organizations have leveraged the integration of Exchange and AD by also combining their administrative teams, thereby completely avoiding this scenario.
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