BizTalk 2013 R2 will be supported in v6.0, which does not have a scheduled release date. I hope to have a stable beta within the next couple of months. I can't say whether you can continue using MSI's from v5.5 with 2013 R2 since I haven't done any compatibility testing. However, I'd be inclined to say yes because 2013 R2 just isn't that much different from 2013.
Thanks,
Tom
Thanks,
Tom