I ended up defaulting to Skype anyway, because everybody else uses it and it feels more integrated, if that makes any sense. It handles logging a lot better as well. It's a shame that its Win8 app is still buggy and limited, but it seems to be getting there and the desktop client is still pretty nice.
What bugged me about WLM was that it felt incredibly inconsistent between versions and also to the rest of the Windows experience. That and it always felt like it was lacking something. That and, let's face it, nobody really needed to use custom fonts or a lot of the other features of the program. Really, as long as Microsoft are intent on porting across features which were exclusive to Messenger (including the older games), it shouldn't be a huge problem.
What does bother me is that, currently, there's no way to organise contacts by protocol in the Win8 app. I can imagine the desktop client being about as painful, once everything's merged. Still, it's better to focus on one client when the Skype side handled calls better and the WLM side handled messaging better. I'm curious to see what comes of this.