We decided to implement BizTalk rather than writing custom solutions in order to standardize code and make it easier/quicker to bring people into the development team without having to sift through tonnes of code in order to determine how certain processes work.
We also run a SharePoint Portal so we plan on integrating BizTalk into SharePoint in order to provide information about systems to non-IT staff who are stakeholders for a particular system.
Once you get past the learning curve of BizTalk I believe its often faster to develop/deploy a BizTalk application than a custom .NET application.
I think the improvements made between 2004 and 2006 and the "quick" release of 2006 R2 is an indication that MS is behind the product and will continue to support and enhance it.