To help avoiding long investigations:

Visual Studio 2012 Intellisense was not working for server controls when edinting ascx files in a WAP project. The error message was something like Unrecognized tag prefix or device filter 'asp'. It worked fine in the code behind or for normal HTML tags.

I found the solution here on stackoverflow. After commenting out the "controls" section in these lines in the web.config

<pages> 
  <controls> 
    <add tagPrefix="asp" namespace="System.Web.UI" assembly="System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" /> 
    <add tagPrefix="asp" namespace="System.Web.UI.WebControls" assembly="System.Web.Extensions, Version=3.5.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35" /> 
  </controls> 
</pages>

everything is back to normal - until you try to edit the files with VS 2010 - then you have to remove the comments again.

Hope it helps someone...

Best wishes
Michael