We've been using BizTalk since version 2004, and now have a mix of versions 2006 R2 and 2004 running. I found that the learning curve was quite severe, and development time for solutions is not always quick. Those are definitely shortcomings. Where BizTalk really excels is in its fault tolerance, gauranteed delivery, and performance. You can rest assured that data will not get lost. Retry functionality and fault tolerance robustness is baked in so generally speaking if systems are down BizTalk will handle that and successful delivery will occur once systems come back on line. All these issues such as downtime, etc that are important in an integration scenario are handled by BizTalk.
Further, generally speaking when developing solutions BizTalk abstracts the communication protocols and data formats of the native systems by dealing with everything as xml, so when developing solutions, you typically don't have to wrote code specific to those systems, you use the BizTalk xml framework.
In the last year, we've implemented a java open source engine called Mirth for our HL7 routing. I found that for HL7 purposes, the HL7 adaptor for BizTalk is a challange to work with. Management dicated that we use Mirth for HL7 routing. Where BizTalk falls down in terms of learning curve, Mirth makes up. It is far easier to develop a solution. The problem with mirth is that it doesn't really have any gauranteed delivery. Most of the adaptors (except for hl7) have no retry functionality so if you wanted that you'd have to write your own. Second, Mirth can lose date if it goes down. I would call it very easy to use (although there is no documentation) but I'd be hard pressed to call it an enterprise solution. I'm going to check out jitterbit which was mentioned by someone else.
