We have user’s that have multiple emails accounts due to the need to send out email and receive emails with the same domain/service provider name eg. @maindomain / @domain1 / @domain2 etc.
And some of our users have up to 5 different emails that they need to manage currently and with us moving to office365 I can understand that this will eventually be a huge issue with licensing, searching and managing.
In my mind the best option to correct this issue would be by setting up a way for these users to send and receive emails from their main account (So not an alias, as that is one way). This option needs to be functional for both OWA/365 and desktop outlook. That way they can use one mailbox and the user can change the outgoing emails to the domain and the external party won't see the difference.
We are using hosted exchange right now, in the future planning on moving to Exchange online.