I sat in on this session yesterday at Convergence, presented by part of the Microsoft FRx/MR team. I personally have not yet had to migrate any clients from FRx to MR but I know the time is coming soon.
The good news is, if you follow the upgrade guide provided by Microsoft with the MR software (and additional documentation which can be found in the KBs on CustomerSource and PartnerSource) the upgrade looks like a relative piece of cake. Likewise, the Microsoft folks are reporting a very short ramp to get your people up to speed on Management Reporter. The similarities between it and FRx are strong, so it should be a pretty easy transition.
One disadvantage that exists right now in MR is that you can't email reports like you can in FRx. That capability may be included in future releases of MR, but that's going to be determined by the user community. The MS team reports that the focus group they use to provide input into the features that are included in the future hasn't indicated a strong desire for email capability within MR.
If you're using MR right now and or are planning to in the near future, you might want to check these links. The first is a link to the LinkedIn Management Reporter Users Group. The second link is to a You Tube video posted by Microsoft on the Management Reporter tool.