Let's actually have counters and not things that find it hard to switch in on any of it's attacks.
Lando-T
Clefable
Mew
Rotom-W
Skarmory
Slowbro/Mega Slowbro
Celebi
All come to mind.
I've been doing some damage calculations, and, well, lets look at some results.
252 Atk Mega Lopunny Return vs. 252 HP / 252+ Def Mew: 66-78 (31.8 - 37.6%) -- 0.2% chance to 3HKO after Leftovers recovery
Okay, so Mew (and Celebi) can tank Lopunny pretty well, and then do the KO it with Psychic?
4 SpA Mew Psychic vs. 0 HP / 0 SpD Mega Lopunny: 108-128 (77.1 - 91.4%) -- guaranteed 2HKO
No. So, that means that, a completely physically bulky Mew/Celebi will take three hits from Return (if they switched in). Leftovers will save them, but just they will be easy pickings.
Lets try Rotom.
252 Atk Mega Lopunny High Jump Kick vs. 252 HP / 252+ Def Rotom-W: 79-94 (50.3 - 59.8%) -- guaranteed 2HKO
Rotom does not want to switch in, even if it has a Sitrius Berry, mainly because Hi Jump Kick will bring Rotom down into the range of a Burned Lopunny.
Okay, lets see about Landorus.
-1 252 Atk Mega Lopunny Ice Punch vs. 252 HP / 252+ Def Landorus-T: 92-112 (46.9 - 57.1%) -- 37.5% chance to 2HKO after Leftovers recovery
This is the a more uncommon physically defensive Landorus. Look at that. 37.5% chance to 2HKO. Okay, but after a Return or even Hi Jump Kick, with Leftovers, and with the lowest Hi Jump Kick doing less than it could (2% less)
-1 252 Atk Mega Lopunny Ice Punch vs. 252 HP / 252+ Def Landorus-T: 92-112 (46.9 - 57.1%) -- 87.9% chance to 2HKO.
Landorus using Earthquake:
4 Atk Landorus-T Earthquake vs. 0 HP / 4 Def Mega Lopunny: 82-97 (58.5 - 69.2%) -- guaranteed 2HKO
Okay, Landorus doesn't want to switch in to Lopunny, even with that Intimidate. Clefable, anyone?
252 Atk Mega Lopunny Return vs. 252 HP / 252+ Def Clefable: 79-94 (39.1 - 46.5%) -- guaranteed 3HKO after Leftovers recovery.
Can Clefable OHKO Lopunny?
4 SpA Clefable Moonblast vs. 0 HP / 0 SpD Mega Lopunny: 108-128 (77.1 - 91.4%) -- guaranteed 2HKO
No.
Skarmory Time!
252 Atk Mega Lopunny High Jump Kick vs. 252 HP / 252+ Def Skarmory: 66-78 (38.3 - 45.3%) -- guaranteed 3HKO after Leftovers recovery
And for Skarmory using Brave Bird
4 Atk Skarmory Brave Bird vs. 0 HP / 4 Def Mega Lopunny: 120-144 (85.7 - 102.8%) -- 18.8% chance to OHKO
Okay, so Skarmory does good. Finally, Slowbro/Mega Slowbro
252 Atk Mega Lopunny Return vs. 252 HP / 252+ Def Slowbro: 61-73 (30.1 - 36.1%) -- 52.4% chance to 3HKO (on the turn it switched in)
252 Atk Mega Lopunny Return vs. 252 HP / 252+ Def Mega Slowbro: 43-52 (21.2 - 25.7%) -- 1.1% chance to 4HKO (when it Mega Evolves, so about 60%)
And Slowbro can do:
4 SpA Mega Slowbro Scald vs. 0 HP / 0 SpD Mega Lopunny: 58-70 (41.4 - 50%) -- 0.4% chance to 2HKO
4 SpA Mega Slowbro Psyshock vs. 0 HP / 4 Def Mega Lopunny: 120-144 (85.7 - 102.8%) -- 18.8% chance to OHKO
So Slowbro and Mega Slowbro are the way to go. This doesn't even factor in Stealth Rocks or Spikes, but it does factor in the fact that they would switch in to an attack, which, as you say, a good counter should do. And the fact that it can heal up any damage done, or has a decent amount of life for upcoming opponents, makes a really good counter. Mega Slowbro all the way baby. If you see an error, please, let me know.