The question is should there be a middle ground between keeping the product trivially simple, or cramming an increasing amount of features to satisfy power users. Either extreme works well for a specific subset of Apple's user base; a middle ground is more prone to leaving everybody confused and/or unsatisfied.
I have zero UI design experience so can't really chime in. Maybe a toggle option inside a menu that swaps app modes? Leave it off and you have a very basic Notes app; toggle it and you get all the bells and whistles, tags, folders, parsing... But this totally causes the problem you describe in your last paragraph.