I don't see how Clefable can counter or even check Mega Salamence. The damage calc is broken right now but I'm pretty sure the standard Mega Salamence can at least 2HKO Bold Clefable with a DD under its belt while Clefable can't OHKO back.I personally prefer using Clefable to counter many of the new megas such as megamance, mega gallade, and even mega sableye.
It still checks since it can switch in while Clefable uses Calm Mind, Softboiled, Stored Power, or Flamethrower.Greninja doesn't want to switch on a moonblast though.