In the migration scenario, you get the benefits of native mode: day one. Also, setting up your new environment...
and working out all the particulars without affecting users can be appealing. With this extra advantage and risk mitigation comes some additional work.
Once you set up the brand new Active Directory and Microsoft Exchange infrastructure -- bringing over your users isn't as easy as the in-place upgrade. But remember -- you had the advantage of setting up and configuring your new environment without having any production users in the way of your "production testing" of the new system.
To move over the user accounts, you will need a free tool like Microsoft's Active Directory Migration Tool. This only brings over the user accounts, so to update the links on the user workstations, etc. -- you may consider a third-party tool.
Once you have the user accounts in the new forest, you also need to bring their mailboxes along. You can use the native tool, ExMerge, to export and import the data across Exchange 2003 organizations.
This will require some coordination, probably over a weekend, so you can move everyone. (I'm again assuming you don't have 10,000 users, but are a small to medium size business,)
Last tip: Don't forget to switch over your MX record, or when you decommission the last of your old infrastructure, users will complain about not receiving external e-mail.
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