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When deleting accounts, give an option to archive all of a user's email/calendars/data into a compressed format with the option to redownload it later.
Don't delete a user's Google Docs when deleting their user account; reassign them automatically to somebody else in the org, or don't require that docs have one explicit "owner".
Don't count "suspended" accounts toward the paid user limit.
Allow admins to force all domain users to enable 2-factor authentication
Allow arbitrary email addresses, not tied to accounts or groups, that can route mail to other addresses.
Allow the list of groups to display more than 30 groups per page (preferably "all" would be an option).
Make the entire admin interface much faster. As is it can be slow for a number of actions.