I have two skinning-suggestions which I think would be pretty neat to have.
1. Before it's too late, it would be very handy to split up Messenger skins and Messenger Plus! skins. This is because almost no skins actually skin Messenger Plus! windows, and it would be pretty cool if we could mix up one Messenger Plus! skin with one Messenger skin. For example if the skin-developer doesn't have time to make a Messenger Plus! skin, he could just recommend the users to use a black Messenger Plus! skin, which would fit to his black skin. I think this is pretty important, because I'm sure you've noticed that no modifications are made to Messenger Plus! at all (except for the status icons), and Patchou has probably put a lot of time in it, to implement Messenger Plus! skinning.
2. Allow small scripts to be executed within skins. This one isn't as important as the previous one, but it would be very useful if we could include small scripts with our skins. For example, if we want a alpha-key for our window (Win32 transparency feature for Windows XP and above), we could implement it without having to recommend users a script for download. We could also make the skin settings-window more useful, with different types of options, including custom pictures (a file-selector) maybe. I would probably also make a very nice per-pixel transparent Vista-skin.