I think that you should set the TargetVersion attribute to the VSExtension:VsixPackage tag. I set TargetVersion="11.0" for installing the vsix for VisualStudion 2012. For two versions of VisualStudio you need two VSExtension:VsixPackage elements. I use one vsix for two VisualStudio professional and VisualStudio Windows Express (vswinExpress). Here is my code:
<Component Id="AlvenosVsix" Directory="VSIXES">
<VSExtension:VsixPackage File="AlvenosVsixFile" PackageId="AlvenosProjectTemplate..330e64ab-f5eb-4211-8fbc-d88485dc13e2" Target="professional" TargetVersion="11.0" Vital="yes" Permanent="no"/>
<VSExtension:VsixPackage File="AlvenosVsixFile" PackageId="AlvenosProjectTemplate..330e64ab-f5eb-4211-8fbc-d88485dc13e2" Target="vswinExpress" TargetVersion="11.0" Vital="no" Permanent="no"/>
<File Id="AlvenosVsixFile" Source="ClientAndServerBuilder/Vsixes/Alvenos.vsix" />
</Component>