Your intentions with Visual Composer..
I would like to know your intentions with Visual Composer. If you plan on always keeping it "secondary" to your Muffin Builder then I will probably be better off creating websites with a different theme as, going forward, my clients really do prefer Visual Composer and makes it easier to train them if it is all kept as Visual Composer.. rather then having to teach them both.
But if you plan on improving it so that it has all the functionality that Muffin Builder does, then I don't mind waiting.
I know you intend on making all your shortcodes usable in Visual Composer, but what about all the row / column options? For example, in muffin builder I can add a background to a row and make it paralax... this isnt available in Visual Composer. Im sure there are 100's of other examples but of course I cannot list them all.
So just as a rule of thumb, do you intend on making Visual Composer just as functional as your muffin builder?