Hi,
Grab the latest desktop installer, but don't uninstall your current version. This way you can keep your settings, but you won't have to go through the older, inaccessible skype.
The newer versions of skype still use chats as listboxes and such, but you can enable compact mode to have them pop up in a seperate window.
Also, NVDA now announces if you have unread messages. What's more, Microsoft themselves have actually mentioned NVDA on their skype website, in the accessibility section. Also, narrator gets a mention.
I was really surprised, I thought it would be a memory hog, and I just used Teamtalk for months and months, but what with msn going down very soon, I thought I'd give skype another try. I wouldn't have mentioned it if I didn't like it.