The issue is not with the rating system. I whole-heartily agree that content creators shouldn't be censored because of parents inability to, well, parent their kids. The problem lies with making direct ties between something clearly aimed for families with something clearly aimed for adults.
Imagine, for a moment, that Nintendo made a violent video game (Think Ninja Gaiden 2 or something) where the player character is slashing down badguys in a fantasy setting. They throw a couple easter eggs to hint that maybe the game takes place in Hyrule, or another land in the Zelda universe.
Despite the winks and nods for fans, they would never have that character appear in a mainline Zelda game for the same reasons.
