Regarding the GAC question - as you found, the msi only installs Telerik.Web.UI.Design. To install the other needed assemblies you could create a follow up startup task that calls gacutil /i [RadControls InstallationDirectory]\[PathTo Telerik.Web.UI.dll].
Regarding the second question - You can manipulate the features installed with the command line:
[Download Directory]\Telerik.Web.UI_2012_2_912_Dev.msi /q ADDLOCAL=Assemblies40 INSTALLLOCATION="Install location of your choice"
(Assemblies40 is the RadControls assemblies targeting .NET40)
Don't hesitate to write if you have further questions.
All the best,
the Telerik team
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