I've been lately working on an EDI implementation using BizTalk Server 2006 R2 and have enjoyed some peices of it so far. The challenge so far I've faced is with Mapping ... believe me, this isn't as simple as it looks like when you're working with EDI (using BizTalk).
There have been a number of cases with me when I try to do a map using functoids which don't seem to be happy enough to let things work. XSL definitely is a life-saver. Had Microsoft not supported xsl in the maps, I don't think it would have been any possible to do maps for EDI.
If you are struggling with maps, I would personally suggest to go through Apress Pro Mapping In BizTalk Server 2009. This is one of those books which should be by your side always when doing maps.
