Below a list of know bugs, issues, & other quirks* of BizTalk 2013 R2 (mainly CU3) and Visual Studio 2013 (update 4) , but I will update with fixes as the CUs come out or when I know about a new issue, so if you have another one I will add it (and link to it if you have a blog about it) if you let me know. This in addition to the ones listed by Microsoft on Known Issues in Installation, Configuration, and Deployment
I’ve now posted the below article on a TechNet wiki
* My definitions for classifying these are
Bug: Causes negative impact and no known work around or requires a lot of effort to work around.
Issue: Causes negative impact but has an easy or quick work around.
Missing: A feature that BizTalk doesn’t have that would make our life easier.
Quirk: Something strange or unusual but does not cause a negative impact so far as known.