What is the best approach of updating existing Craft installs with new features?
This approach assumes that the individual websites won't diverge from the original blueprint by, for example, modifying sections and fields to suit their specific requirements.

That seems pretty unlikely.

I'd be inclined to stick with the idea of creating a "blueprint" site, to get new websites up-and-running quickly, but ditch the idea of updating previously-created sites whenever the blueprint is updated.