The fact that it doesn't take advantage of the multi-window nature of desktop systems. Everything happens in one single large window — like on an iPad.
In particular, my issue with modern IM app UIs is that the chat switcher is merged with the chat list. You can't have multiple chats that you're currently active in open at once and switch quickly between them. If you switch away from a chat, you have to find it again in the list to return to it, possibly requiring a lot of scrolling and multiple clicks for what could've been one click or even a keyboard shortcut.
In particular, my issue with modern IM app UIs is that the chat switcher is merged with the chat list. You can't have multiple chats that you're currently active in open at once and switch quickly between them. If you switch away from a chat, you have to find it again in the list to return to it, possibly requiring a lot of scrolling and multiple clicks for what could've been one click or even a keyboard shortcut.