I don't really see what is wrong with the fonts...
Times New Roman is proprietary and almost all windows vista and 7 fonts are proprietary so don't be surprised if a proprietary software like skype (owned by M) have bad fonts.
Anyway you can still download a `replacement` for times new roman, which I think is really really badly rendered in GNU/Linux or BSD.
On the other hand, tons of fonts are really cute and you can try them. (I personally use arial if you want to know)
Moreover, You can check antialiassing and other of those kinds of render options.
Let's just say that *nix have some problems with fonts and it's because we are invaded by windows.