Your web-scoped feature needs to be explicitly added to the <WebFeatures>
section of your web template, see below:
<Project Title="Custom Site" ListDir="$Resources:core,lists_Folder;" UIVersion="4" xmlns:ows="Microsoft SharePoint">
<NavBars>
</NavBars>
<Configurations>
<Configuration ID="0" Name="CustomSite" MasterUrl="_catalogs/masterpage/v4.master">
<Lists>
</Lists>
<SiteFeatures>
<!-- "Custom Site" Web Template Feature -->
<Feature ID="00000000-0000-0000-0000-000000000000" />
</SiteFeatures>
<WebFeatures>
<!-- Custom List Instance Feature -->
<Feature ID="00000000-0000-0000-0000-000000000000" />
</WebFeatures>
</Configuration>
</Configurations>
</Project>
If you have done this, however your feature is still not being activated, do the following:
- Check the SharePoint log files to see if it has attempted to activate your web-scoped feature. Your feature may be throwing an exception and not completing the activation phase as expected.
- Using either SharePoint Designer or PowerShell, check that your custom web template has in fact been used to create to your new subsite.