I think history shows that the distinction is important; some agencies are well-adapted to handling these issues, while others are not. I'm still undecided, but I've read that the FCC's action in 2010 was a political power grab by friends of the administration (e.g. Google). On the other hand, the FTC has a strong history of trust-busting, e.g. AT&T in 1984, making it the stronger contender for actually handling net neutrality in essence. Whether or not that's true (see other comments), I'm not sure.