It may also be that Motorola is trying to get the device out the door as soon as possible with a more modern OS. Windows Mobile 6.1 is a bit long in the tooth since it is visually almost indistinguishable from WinMo 5, a platform that shipped nearly 4 years ago. WinMo 6.5, which is substantially updated, was just completed this month, but it will be three months or more before the first devices start showing up.
If Motorola wanted a phone out before then and wanted a more modern looking OS than WinMo 6.1, they could have switched to Android months ago if they wanted to guaranteeing a Q3 launch.
Motorola and Microsoft aren't parting ways. Motorola said months ago, long before MS would have liked, that WinMo 7 would be out in 2010 and Moto would be a key player in that market.