Actually that Full Screen Mario game for browsers with level design capabilities got taken down (but has since been mirrored) and Super Mario Maker was announced shortly after.
Which I am sure Nintendo either stole the idea or someone already beat them to it. Actually, SMBX already beat them to it and it is still an obscurity due to how hard it is to use.
Mate, Mario World had a very active rom hacking scene well before either of those, there's also games such as Little Big Planet which also do the same basic concept and also predate them. Even with Nintendo you had shit like WarioWare DIY, the Mario vs Donkey Kong series, or even Excitebike which all have editors. Making a Mario game with a level editor isn't rocket science, the appeal of level editors has always been apparent. While something like Full Screen Mario certainly could've been one reason for doing Mario Maker, it wouldn't have been the only one by any measure.
As for projects that are taken down due to just becoming too popular, that is why I think it is also an attempt to save face too. It would be quite shameful to be outdone by a group of fans would it not?
I mean, I guess, but they can do that if they want to, something like Little Big Planet's better in many respects to Mario Maker, but it doesn't use their IP, so they don't care. Granted it's not a indie game or anything, but I think it still illustrates my point, the problem's using the IP and assets. Another good example of that I can think of is Terraria, same creator as SMBX, but it use original assets so they don't care what he does or if he puts it on their platform.
