We evaluated BizTalk at our company and were really disappointed.
We are using IBM WebSphere Transformation Extender (which has lots of (other) problems, too) and the mapping tool of BizTalk is a joke in comparison to WTX.
The graphical tool is not really usable for complex mappings (we have schemas with a few hundred fields in repeating groups) and if you do more than the usual "concat first name and last name to name" mappings, you will be tired of the graphical approach (for example the arguments of the functoids in the graphical mapper are not labeled and the order in which you connect fields to these arguments is important).
The XSLT-Mapper was usable but not really convincing, and even the microsoft rep told us to use a tool like XMLSpy for XSLT and load the resulting XSL file into BizTalk.
A third approach to mapping is to use C#-Code for the mapping, which was not acceptable for us as a general approach (we don't want to teach everyone C#).
In addition to the mapping tool we did not like the deployment in BizTalk. In order to deploy your process, you need to make lots of settings in different tools and places. We had hoped to find a mechanism like a WAR file for Java Web Applications in BizTalk, so that you can give one archive for your whole process solution to your administrator and he can deploy it.