Ignoring the glitch, I've got no problem with the merge in principle, but at the moment, the Skype client is missing (or doing a good job at hiding) more than a few features from Windows Messenger. Off the top of my head: Email notifications, Custom Fonts, Tabbed conversation Interface, Send Email, Photo sharing, sending files to MSN Contacts, Remote Assistance, nudges, and group chat.
I'm not the only one pinning for features, either: http://community.skype.com/t5/Live-Messenger/Will-Skype-be-updated-to-include-classic-msn-features/m-p/1183778
As a video client, Skype is great, but at the moment, as an IM Client, it feels like a downgrade from MSN Messenger, and leaves a lot to be desired, with only vague promises of the shortcomings being addressed (http://community.skype.com/t5/Live-Messenger/No-email-notifications-after-merging/m-p/1184924/highlight/true#M71)
Coupled with the fact that Microsoft quietly killed off Yahoo IM Support in December (http://answers.microsoft.com/en-us/windowslive/forum/messenger-people/messenger-to-yahoo-chat-interoperability-is-no/1941a832-3b78-4cb8-9a9f-ec2e36ca4684), it's clear Microsoft are railroading users down this path to make their Skype investment worthwhile, with scant regard to what they want - A textbook case on how to mismanage migration.
"The New Messenger is better"
"How? Aren't there import problems? It's missing features. Are you adding them? What about my non MSN Contacts?"
"...The New Messenger is better"