I just finished upgrading to R2 on my Vista x64. So far everything seems to be running fine, except....
Business Rules Engine:
There is a new location for the assemblies now. On Biztalk 2006, the location for the BRE assemblies was this
c:\Program Files (x86)\Microsoft BizTalk Server 2006\Microsoft.RuleEngine.dll
However, after removing my 2006 version, and freshly installed the R2 version, I have to go and recompile all of my assemblies that had a reference to the Microsoft.RuleEngine. The new location is
C:\Program Files (x86)\Common Files\Microsoft BizTalk\Microsoft.RuleEngine.dll
Other than this, everything seems to be running smoothly (Orchestrations, pipelines, etc...) so far. I will update this post as I find any more gotchas (if any... ;)