System Center App Controller is a self-service portal which allows non-IT staff to deploy virtual machines to clouds on-premise, in Service Provider clouds or in Windows Azure.
Windows Azure supports both Windows Server and Linux as guest operating system in a virtual machine.
However when using App Controller 2012 R2 those Linux images are not available for deployment. Three different Linux images are shown but are greyed out.
When using the Azure Management Portal a choice of 9 different Linux images is available: various versions of Ubuntu, CentOS (Openlogic distribution), SUSE and Oracle Linux.
This is caused by a limitation of App Controller. When preparing a deployment of a virtual machine App Controller creates a so called Configuration Set. This is an XML file which has information like the computername, user account and password or certificate. When user input has been recieved App Controller transmit this information to Azure.
At this moment App Controller 2012 R2 lacks the ability to deploy Linux images.