A beginner would not want to break compatibility with every tutorial/instruction manual. They would be faced with decisions about the placement of shortcuts they're not even sure what they do. They definitely wouldn't have the perspective to create logical families of shortcuts.
So of course the solution is to suffer the bad shortcut placement in Emacs long enough to not need tutorials and fully understand what you're doing, then throw all the intuition you've gained out the window by remapping everything.
Oh, the beauty of emacs, the self-documenting editor...This is highlighted at the top of the built in tutorial if you change your keybindings:
>NOTICE: The main purpose of the Emacs tutorial is to teach you
the most important standard Emacs commands (key bindings).
However, your Emacs has been customized by changing some of
these basic editing commands, so it doesn't correspond to the
tutorial. We have inserted colored notices where the altered
commands have been introduced. [More]
[More] is a list of the default keybinding, the command, and how to access the command in "your" emacs.
The keybindings are also changed throughout the entire manual (C-h i) I believe.
Would it maybe be useful to have some framework for creating tutorials inside emacs? In that case, the tutorial could just check which shortcut(s) are defined for a given command, and update the tutorial text to reflect that.