I can think of few reasons to use Microsoft's Windows Defender over Microsoft Security Essentials. Both are free, both protect against spyware. With Microsoft Security Essentials you also get anti-virus protection.
A comparison chart at Microsoft illustrates the difference between the two programs.
What follows is an old review which still applies to Windows Defender and equally to Microsoft Security Essentials.
Old Review
A very easy to use anti-spyware program. It offers real-time protection from spyware and malware brought to you by the company that makes the operating system being infected. The next version of Windows (Vista) will have Windows Defender built-in.
Hands-Off, Automatic Protection
A great choice for the non-technical users. It automatically updates it definitions and automatically runs full system scans.
Windows Defender (formerly called Microsoft AntiSpyware) notifies you when a potentially dangerous change is made to your system. Thanks to a community-backed "white-list" of programs considered safe, you generally don't need to approve these changes.
New Packaging of Another Company's Code
Microsoft released the first beta version in January 2005. But the core software dates back to 2001 when it was known as Giant AntiSpyware.