As of yesterday we're fully off Rackspace and onto Microsoft-direct Office 365! Our solution was:
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Through Rackspace's Office 365 page, buy Rackspace-managed Office 365 licenses for all the users. These show up in 365 Admin as "Reseller" licenses, as opposed to licenses purchased directly from Microsoft which show up as "Commercial direct".
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Use Rackspace's email migration tool (which is actually BitTitan MigrationWiz reskinned for Rackspace) to migrate all of the Rackspace/Hosted Exchange addresses to 365. This tool comes bundled with Rackspace-managed 365 licenses, but not Microsoft-direct licenses.
I tried 4000 ways of migrating with Office 365's built-in migration tool and got nowhere, and Rackspace's support was no help. If you look around you'll see that BitTitan is recommended pretty much universally for this. It's fantastic that Rackspace's 365 licenses bundle it.
Note that it seems once you've migrated a mailbox, if you migrate again then BitTitan only picks up any new items that came in since your last migration. So while the first migration may take a day or two, any follow-up migrations should just take minutes.
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Through the Office 365 Admin (NOT the Rackspace 365 page), buy Microsoft-managed "Commercial direct" Office 365 licenses for your users.
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Through the Rackspace 365 page, deactivate all the Rackspace "Reseller" Office 365 licenses.
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Through the Office 365 admin, assign all your shiny new "Commercial direct" Microsoft licenses.
Done! In short, you're purchasing Rackspace "Reseller" 365 licenses just long enough to use their bundled email migration tool, then immediately switching out those licenses for "Commercial direct" licenses from Microsoft. If you do the last 3 steps quickly then your users won't lose any data. I think the grace period is several days, but did it ASAP just to be safe. On our last billing statement Rackspace seemed to charge us only for the time we actually had their 365 licenses, which was not much. Hopefully Rackspace doesn't start setting contract minimums for those licenses. Also note that once all of your Rackspace subscriptions have ended you will no longer be able to access your Rackspace account.