I've stuck to the desktop version. I tried the Metro version, it looks great, but it's not feature complete (e.g. screen sharing isn't supported I think), and I prefer having the video of the person I'm calling in a window, not full screen.
Yes, you can sign in with your Microsoft Account now, and see all your Messenger contacts in Skype and chat with them. If you have a Skype account, you can merge the two (and the Metro Skype app forces you to do this, as you cannot sign in with an old-style Skype account). On the desktop app I don't think you need to merge, you can just log in with both simultaneously (though I'm not a 100% sure since I did merge them when trying the metro app).
The only advantage of the Skype metro app are the background notifications for messages or calls even when the app isn't running, whereas the desktop Skype needs to be always running just like Messenger.
If all you do is text chat, by the way, you might as well use the Messaging app in Windows 8 and not bother with Messenger or Skype.