Given that Paint.net's equivalent operations are not exactly the same as MS Paint's tools, it would be unreasonable to make a "use MS Paint shortcuts" option. Even the two that you mention don't have perfect matches in the Paint.net interface. Inevitably, if Paint.net mimicked MS Paint shortcuts, there will be confusion among MS Paint users looking for features and not finding them where they "normally" are. ("normally" is in quotes because MS Paint is really low-bar to be used as a standard for image-editing software)
Also, Paint.net is not in any way meant to be a copy of MS Paint. It's more of an alternative to Photoshop and GIMP. So it makes sense that the shortcuts are not much like Paint.
I don't know if there are any plans to add a shortcut editor, but as far as I can tell (maybe I missed something), Rick has not indicated any plans to add such a feature.