One of the hardest and sometimes most frustrating experiences with migrating from Notes to Exchange is using the Lotus Notes connector. Often a migration can take months if not years and frankly the Notes connector just isn't meant to be run that long.
Well there is another option. The Notes connector basically provides two functions, it synchronizes Active Directory with the Notes directory and provides mail routing functionality so that Notes users can send email back and forth to Exchange users. So instead of using the connector to synchronize the directories, you can use MIIS to perform the same function. You can even enhance your directory synchronization. For example, if you have a lot of applications still written in Domino databases, you will need to keep those pesky Notes clients around for quite some time. Provisioning a new user in Notes is a pain because you have to generate a Notes ID file. However with MIIS and a little coding you can have the Notes ID file generated automagically. So what about mail routing? Instead of using the Notes Connector, you can just use SMTP routing to route mail back and forth between the two mail systems.
If you are interested in more specific details on how to do this, check out this great blog post:
http://alextch.members.winisp.net/DominoExchangeSMPTSharedSpace/DominoExchangeSMTPSharedSpace.htm