True. That said, for the Princess Rescue game, the major issue I think was that AtariAges were making money off the game (even if it was to cover cartridge production costs, Nintendo has no proof) and I heard that Nintendo are really copyright not(C) when it comes to their music, and Princess Rescue almost had an identical replica of the SMB1 theme.
I bet that if the game was released with different music and recolored Mario sprite, they would not have gotten any problem, since Nintendo would have gotten no proof from the graphics that it's meant to be a Mario game.
Still, it's insane that companies would care this much about fan games made for such old console. It reminds me when Parker Brothers sent a cease and desist letter to the guy who made Monopoly for the TI-83 in 1998 (although that was resolved I think) or Golden sun in 2005.