Azure SDK is installed but Visual Studio 2012 doesn't see it
Open Programs and Features, locate the 'Windows Azure Tools for Microsoft Visual Studio 20xx' (where xx is the version of Visual Studio you are experiencing the issue with)
Right click and choose Repair.
Once the repair is complete, re-open Visual Studio, search installed templates for 'Cloud' and the 'Windows Azure Cloud Service' project should appear, confirming that the issue is resolved.
I had this same problem. Rebooted, still couldn't get it to recognize the Azure SDK 2.1 for VS 2012.When I right-clicked, I only had the options to Uninstall or Change. I chose Uninstall, and another windows popped up asking if I wanted to repair. I chose Repair and then finally Windows Azure Cloud Service appeared.
I've had similar issue few days ago. Both, VS10 and VS12 installed on Win 7 machine. And VC12 didn't see azure so I followed steps from VS12 and installed it again and then it still didn't work.
However, after VS12 and system restart it actually worked.