If you don't mind screwing with the default files., you know that New Projects are controlled by the NewProject.agk in the Media Folder of the AppGameKit Installation...
By default it just includes and updates the main.agc that's available in data\templates but you can add any number of custom .agc to that folder and include them within the newproject.agk ... then all new projects will use that as the basis.
Mind I couldn't tell you all of the Template { } that are applicable., as TGC doesn't exactly provide any help or information on that.
I'd agree though... it would be nice if we could have Multiple Custom Templates., so say for example I wanted to make an AppGameKit VR App... instead of either manually, macro or batch file setting up the base project, copy the files, etc.
Instead you could choose "New Project" and it's one of the New Project Options.
I mean given there is something like AppGameKit VR which is a "Official" Plug-In (might be 3rd Party Developed, but they still market and retail it as if it's something that was in-house)., you'd think they'd have added such functionality.
It'd be a really powerful tool for both Plug-In Developers and improve the Quality of Life aspect of the Editor.