Downgrading from BizTalk 2006 R2 to plain 2006 doesn't seem to be a well-trodden path. It's not ideal, but if you have to do it, the following steps should get you there:
- Uninstall BizTalk 2006 R2 from Add/Remove programs
- Try to uninstall Enterprise SSO from Add/Remove programs*
- Remove the BizTalk databases (detach the databases in SQL Server, then remove the MDF and LDF files)**
- Delete all the BizTalk-related SQL Server Agent jobs
- Unregister the Notification Service for BAM Alerts
- Install & Configure BizTalk 2006
* - I had issues with SSO where the uninstall kept crashing halfway through. Eventually removed it by selecting "modify" then removing the core components – "Server" and "Administration". Then it was happy to reinstall from the 2006 setup.
** - you can unconfigure the instance instead, but this way lets you backup the data files, in case you think you'll need them.