Will Windows Workflow Foundation Replace BizTalk Server ?

The answer is no. Here is an excerpt from David Chappell's excellent whitepaper: Introducing Microsoft Windows Workflow Foundation: An Early Look 

Use Windows Workflow Foundation when:

An application will itself host workflows. Windows Workflow Foundation lets workflow be built into an application, allowing the workflow to be deployed and managed as a native part of the application. Because it's focused on integrating diverse applications rather than providing a general workflow framework, BizTalk Server always runs orchestrations within the BizTalk Server process.

The business process being implemented requires human workflow. BizTalk Server addresses system workflow, and so it lacks Windows Workflow Foundation's support for things such as state machine workflows and dynamic update. A scenario that requires both human workflow and more complex system integration services could be addressed by using Windows Workflow Foundation and BizTalk Server together, however. For example, the Office "12" support for document-centric workflows, based on Windows SharePoint Services, might be used for the human aspects of the problem, while BizTalk Server handles the system integration aspects. The two can interoperate using the BizTalk Server Adapter for SharePoint.
The workflow will execute on a client system. BizTalk Server is a server-focused product, and so it's less well-suited to run on desktop machines.


Use BizTalk Server when:

Solving an EAI problem that requires communication with diverse applications on diverse platforms. Because of its focus on cross-platform integration, a large set of adapters is available for BizTalk Server that allows communication with a range of other software. Windows Workflow Foundation is focused solely on workflow, not EAI, and so it doesn't provide these things.
B2B services are required. Windows Workflow Foundation doesn't address this area, while BizTalk Server provides tools for working with trading partners, accelerators for RosettaNet, SWIFT, and other industry standards, and more.
BPM services, such as Business Activity Monitoring (BAM), are required. While the Windows Workflow Foundation tracking infrastructure can be used to create these services, BizTalk Server provides important extras, such as tools that let information workers define their own BAM views.
A complete management infrastructure and support for increased scalability are required. Unlike Windows Workflow Foundation, BizTalk Server includes a full set of tools for administering and scaling a production environment.