Steps to reproduce it

1. Fresh installation of Jenkins (Jenkins ver. 2.0-rc-1)
2. We choose Recommended Plugins option
3. Items availables are: Freestyle project, Pipeline, External Job, Multi-configuration project, Folder, Multibranch Pipeline

Where is GitHub Organization?

Only if we acces to Manage Plugins >> Installed (tab) we see the following message:

Warning: This Jenkins instance requires a restart. Changing the state of plugins at this time is strongly discouraged. Restart Jenkins before proceeding.

After restarting, we can see the item GitHub Organization.

I see here two problems:

1. We need to restart Jenkins after the wizard installation
2. The warning message is completely hidden. It is difficult to know that you have to restart.