April 22 Update: New blog post about the decision tree on server team site - http://communicationsserverteam.com/archive/2009/04/13/409.aspx
Very important: (from the R2 help file)
If you decide to migrate your global settings to the Configuration container and you plan to migrate from a prior version of Office Communications Server to Office Communications Server 2007 R2, you must perform the global settings migration first. Once you upgrade to the Office Communications Server 2007 R2 Active Directory schema, you can no longer use this tool to migrate your global settings.
I have LCS 2005 SP1 in my topology so you can see the decision I will make from this flow chart – no change.
Quick update -
Because I knew of this requirement I never ran the Schema Prep as I didn’t want to get caught (also I didn’t have undo disks configured in VMs and didn’t want to restart (lazy)), the setup routine will notify you of this new requirement:
Edit January 14 2009
Fred was asking about the reason and apparent vague performance reasoning so let me post what is in the documentation for RTM and see if this is acceptable. Fred if this is still not acceptable email me direct so we can attempt a last minute change (no promises as I don't own the documenation effort but do communicate frequently with them).
With Office Communications Server 2007 R2, the recommended container for Office Communications Server global settings is the Configuration container, which is the default container. In previous versions of Office Communications Server, the default container was the root domain System container. Although storing global settings in the System container has advantages, such as faster replication and fewer replicated copies, in centralized topologies, this approach might not perform as well in geographically distributed topologies if root domain availability is insufficient. If you deployed Live Communications Server 2005 with Service Pack 1 (SP1) or Office Communications Server 2007 with global settings stored in the System container and experience performance problems, such as long service start time or long replication delays when you manage global settings, you can migrate from the System container to the Configuration container.