Skype chat is definitely the weakest link the chain for our remote team as well; it's basically unusable beyond a handful of groups. We've been migrating over to IRC for as much as we can. We also briefly toyed with using Mumble (http://mumble.sourceforge.net/) for voip, and while it was pretty compelling in terms of cross-platform stability it never really took off in our organization.
The article mentions only moving off Skype if it's sufficiently advanced beyond Skype. IRC by itself is not, but we've got our own IRC server that adds some important features like indexing and catchup: http://writequit.org/blog/?p=444
Convore is pretty new, but have you tried it for private chats? When it was announced, I immediately started to think how much easier it would be to set up for my non-technical co-workers.
Tying you to the browser is only slightly better than tying you to a single client; textareas are not the kind of place you want to spend much time. I'd be game if there were an Emacs client.
It's true that there aren't a lot of clients out there for Convore yet. There are quite a few Convore projects started on GitHub (https://github.com/search?q=convore&type=Repositories) and more clients are welcome!
The article mentions only moving off Skype if it's sufficiently advanced beyond Skype. IRC by itself is not, but we've got our own IRC server that adds some important features like indexing and catchup: http://writequit.org/blog/?p=444