It seems like al the resources I have been using avoide this at the start then throws in the root as if it's no big deal. The most common is verbs starting with "---masu" and treating that to be the root. Even this site has done it with "aoi" instead of "ao" If I was not cross referencing like I do, this would be incredibly confusing to me when I hear it in a new form.
I, for one, find it far easier to learn the root then build up, but maybe there is a reason I am not understanding as to why this is not common. Is there something I am missing?