So, it seems Microsoft don't actually test things like *using* a server OS before they release it.
The major non MS issue - backup Exec is not compatible, this may be a hotfix for 12.5 or even wait until the next release!
The MS things:
No WSUS, hooray! Put an entry in the list of available roles for something that doesn't yet exist! No WSUS 3.0 SP2 yet, so no WSUS for 2008 R2.
Errors and warnings galore!
I've got it down to 1 error and 5 warnings for the boot of a DC now. There is an error for when Windows boots from the Active Directory Web Services (this seems to be new), seems to be a startup order issue (but happened to both DCs).
A couple of SSL certificate warnings, one for the previously mentioned ADWS which is not fixable, seeing as all the other services are quite happy with the generated DC certificate.
And then there are the annoying things.
Why the Shared documents, with all the sample Videos and music crap? This is a SERVER OS!
You cannot input a name during sysprep - this is not a bug, but a design decision for 2008 R2.
Firewall not opened for KMS server when you use it.
Lots of Hyper-V crap bundled by default, although not enabled.
nslookup a bit broken until you use or disable ipv6
No Exchange support
There are a few nice things:
KMS server now counts VMs towards the activation count
Can't think of anything else specific right now, it's really *very* similar to 2008. The schema updates for R2 and Windows 7 are quite minor over 2008.