I find myself thinking the same thing about every web based IDE/editor - how would you write a graphical application? How would you write a game? I guess its possible to install X on the remote and then somehow stream video over the wire but that seems like a chunky experience.
I guess that's the difference between these and traditional solutions, in a web based IDE you can only write text based applications.
I think web based IDEs are mainly intended for web and server applications. In this situation a game or graphical application would be written in HTML/JS and served to another browser tab.
As a student who moves between boxes a lot I've found this very useful.
The bit that gets me is that I have as shonky and relatively unreliable internet connection and work from home. This is not an issue when my toolchain sits locally.
I really couldn't risk using an entirely online service for direct productivity.
The new version absolutely has SSH workspaces. You can SSH into your own machine or get an SSH box from e.g. digitalocean.com and use that with Cloud9 if you like.
A while ago I wanted to work on a GTK app on cloud 9. With a little work, I was able run a vnc server and install a websockets-based vnc viewer on their infrastructure. It allowed me to view the GTK app in my browser.
I guess that's the difference between these and traditional solutions, in a web based IDE you can only write text based applications.