Even a seamless transition will generate calls to your corporate help desk from some percentage of users, and your help staff would much prefer handling just a handful of these calls per day, distributed over several days. Migrating your universe of users incrementally, by subset groups, should substantially distribute your help desk's load.
Moreover, your organization may have good business reasons to avoid scheduling all users in a single migration event. For example, finance and accounting staff cannot tolerate an interruption at the beginning of a month when they are trying to close the books. Likewise, sales staff should not be interrupted near the end of the quarter when they are striving to meet their quotas, and marketing people need to avoid interruptions near key trade shows or other programs. Migrating users in batches provides flexibility in accommodating these legitimate business needs.
Many organizations designate information-services staff as the first group to migrate, since they typically are the most sophisticated users and therefore provide a solid test of the migration methodology and new system.
Finally, remember that the Deployment Configuration Program lets you configure your users' installation processes differently for different groups of users. Presumably you will want to monitor your users' installations, at least passively, and this will be much easier to do by groups of users who share certain qualities and configuration parameters.