It seems only Facebook is allowed at this time and Yahoo messenger would have to be used via it's downloadable app. As to whether future updates will change is currently unclear. If you open the messenger app up and then click on the settings icon you'll see in the resulting list 'Rate and Review'. Why not tell MS how you think it should be improved?
I've not tried the metro version of Skype and should imagine it's more aimed at the Tablet user than desktop. I tried to find a Yahoo messenger app for PC but it appears there isn't one yet. Windows phone has got one so maybe it'll get ported across?