I'm not really that surprised to be honest. I noticed that MSN hit its peek a few years ago and has just been going down hill ever since while Skype has been sky rocketing in popularity because of its video call features and such.
To be honest the only reason I've stuck with MSN as my primary IM is because of all the different applications I could use to access it, with skype I could only really use the official skype app and maybe one or two others if I'm lucky to find a half decent one. With this change over though and skype becoming the default IM for Microsoft I hope some more apps can let me use skype. If I can get that then I'll be happy with the switch over/merging.