I would suggest taking a look at BAM (Business Activity Monitoring). BAM will allow you to configure tracking profiles to track specific elements of your data(messages). So for instance lets say that you have a PO and you have Customer Name, Address, Price etc in your message and you would like to later Report on this information then BAM is a great solution. You basically configure BAM to track these specific elements and they will be placed into the BAMPrimaryImport database. From there you get BAM Portal (out of the box). This is essentially a Web Portal where you can query your BAM repository. I will admit that BAM lacks in the area of printed reports, it is more an adhoc query tool, but since all of this data is in SQL Server and BizTalk will create the necessary views it is very easy to hook up SQL Reporting Services or even an ASP.Net application to view this info.
Part of the problem with HAT is that you need to keep your BizTalkDTADb database ‘lean and mean’ in order for optimal performance. So I would try to avoid any dependencies on this database for long term reporting needs. The other thing is that unless are querying on promoted properties, HAT wil not give you element level information since your message is essentially stored as a ‘blob’ in the database.
Here are a couple links to get you started