In my experience, not using the targeting system hasn't made any impact on the games' difficulty. In fact, I prefer to go without the targeting system simply because is has a more real feel to it, if that makes sense. Difficulty-wise, though, I don't think it makes a difference.
A true solution to the difficulty issue would simply be implementing the option to choose the games difficulty as so many games do nowadays. Why Nintendo hasn't jumped on this bandwagon with more of their titles beats me. It works marvelously with Metroid... I can see why a Mario game might now need it, but games like Zelda could really do well with it.