The upgrade process to R2 is actually very straigt forward. That is, if your environment is also straight forward.
A collegue of my was presented with an upgrade error when he tried to upgrade the Reporting Server and the Data Warehouse Database in the background.
Eventually it was caused because the user account the SCOM Reporting Server upgrade was started with, was configured as a user on the database without SQL roles.
This takes some time to figure out, especially when you have to work with different teams. A team for SCOM, a team for SQL and for example a team for IIS.
That's why here is a R2 upgrade info list for your convenience:
But most important:
And remember, always create a backup of your database before installing a upgrade.