The plan, according to the Verge, is that the backend of Messenger will be moved over to the Skype client. So you still use your Messenger account and contacts, just in Skype. That move's been happening for a while, and apparently 80 percent of Skype IMs are already through the Messenger protocol. Skype is a better alternative for a lot of people than WLM, and consolidating the number of clients under Microsoft's roof is a good thing.
Messenger remains widely used—according to Microsoft's numbers, it and Facebook are the two most popular chat clients. But, honestly, when is the last time you signed into WLM? So Microsoft has been focusing more on the chat functions in Skype—especially with recent improvements to the client's chat interface—and is even integrating it into its People apps in Windows 8 and Windows Phone 8 in the near future. More here.