Definitely going to be giving cloud9 another shot in the coming days. I spend a fair amount of time (and actually pay for a small slot) on Nitrous.io's PaaS, which I really like. The part about Nitrous.io that really, really, really sucks is the lack of root - you have to install everything (mostly) through "Smart Packages" which is basically just a wrapper around the install I guess, and requires you to build it. Any project with any real dependencies quickly becomes a pain. Some of the newer services (like terminal.com) actually DO give you root, which I'm assuming is OK because it's running on top of Docker? Either way, a nice front-end + root is awesome and I'll be giving it a shot.
On the new Cloud9 version you have full root access. We are now providing Ubuntu 14.04 LTS as a Docker container. Feel free to install whatever you want.