Stu,
WDT has been available in several forms over the years though has most recently been promoted as part of the WebSphere Liberty profile release.
Some benefits of Blue over WDT would include the fact that we support WebSphere servers prior to version 7 along with support for the Portal server, remote deployment & debugging and the community editions, if that matters to you. While not present right now, this year we will also be adding editors for the dozens of IBM deployment descriptors and configuration files.
I don’t believe the WDT tools can be integrated into Blue due to licensing issues, but it’s something we are going to focus on shortly. More detail than I have provided above is due, of course; we are working on a document that compares the soon to be released MyEclipse Blue 2013 release with WDT and the pros and cons of using one over the other. Once ready I will post here.
Thank you for asking,
Brian.