I think it's fair to say that themes should be looked at as examples and nothing more. I also think most people start off EE sites without installing a theme and also most people I know delete Agile Records from their installs from the get go.
ExpressionEngine really makes no assumption about what you want to build for the most part.
With that said, there are a few ways to handle templates. You can turn on the save templates as file feature. More about that can be found here.
You can use a product like Mountee which I won't go into detail here because they have a full site of details. Basically, however, it mounts your templates folder so you can access it via your favorite editor.
You can use something like EE Master Config to setup templates as files using Config Overrides so you don't have to turn on each template as a file. This also has config overrides for moving the default location of the template folder as well. This of course is the more advanced of the three options I listed.
There really is no reason to ever have to edit a template in the control panel these days.