Roar was one sound move that could bypass substitute even before this Gen VI change,and now that i think about it many other sound based status attacks like torment and taunt could bypass substitutes even in Gen V maybe it was turn for damaging moves to follow this Gen.
Taunt isn't sound based. I really wish it was because that would make Mr. Mime all the more useful on my Baton Pass teams, but it is actually a, "Mental Damage Attack" (not to be confused with a Psychic attack). That is why it is cured by Mental Herb.
Anyway, on subject, as someone who has been playing a lot of Baton Pass recently, Infiltrator Chandy
can give me a harder time setting up, but it usually doesn't stop me. If I have enough speed boosts to outrun it, I can pass to Vaporeon or Smeargle, who can come into a choice scarfed Shadow Ball, but proper coverage on a non scarf set can force me to pass to my Clefable sooner than I would like. If I'm not faster, and Mr. Mime or Espeon are in with less than two Calm Minds, I'm in a bad spot. Noivern is easier to handle, because it can't really touch specially defensive Mr. Mime, especially not after a Calm Mind. Scolipede doesn't really
want to take a CB Brave Bird from Crobat, but it can at +2, and only needs to look out for Taunt, which can be deflected by Espeon. In fact, Infiltrator might
hurt their team a bit in those circumstances, because it lets me keep a full health Sub to take any priority moves they could follow up with, while they do pitiful damage to a boosted Espeon or Clefable.
As far as sound based moves go, they are all blocked by Mr. Mime, so none of those worry me, most of the time. Mr. Mime can safely boost against things like Exploud or even Volcrona if it has few to no special attack boosts. It can also come into Roar and Parish Song, which is super helpful. Overall, I don't think that these changes hurt Baton Pass much if at all.