I avoid package gems like the plague. It makes dependency management a gigantic pain in the ass and forces you to target your code to a specific version of an operating system. You can't take a system that works just fine in Fedora and move it to Debian without making sure the gem version differences don't break anything.
In today's cloud-based hosting environment, you want to preserve mobility whenever possible, and Bundler does a better job of managing Ruby dependencies than dpkg/yum does. You can then use configuration management to get a system bootstrapped to a base where all your Ruby projects can run, then Bundler can take care of project-specific dependencies. It's not perfect, a lot of times a project gem will require system dependencies, like MySQL, but the separation of concerns does help a bit.
You should, however, use system Ruby because using RVM / Rbenv in production vastly increases complexity, and because the system dependencies that your gems have will be the right versions. It's much easier now that the latest Ubuntu packages Ruby 2. It took me all of an afternoon to redo the configuration management and provisioning and migrate my projects when Ubuntu 13.10 came out.