I think there will be no engine changes in R2, but this product refresh will include a number of interesting features and enhancements. For example, R2 adds EDI, RFID, WCF and WF BAM Interceptors, the WCF adapter and supports the R2 Adapter Framework and new releases of LOB adapters. You can get more information about what R2 will look like here.
By the way, I'm now working on the WCF adapters that will be released with BizTalk Server 2006 R2. If you have any questions about the adapters, please leave a message.