Take out? Perhaps I don't get it.
Play Mime Jr. and Mr. Mime. Complete shutdown of Take Out. 1 Energy? Nope, 2? Nope, you'd need 3 energy on Machamp to run Takeout. Shumpet is going to 1 or 2 HKO any machamp. Run a Unown G or 2 in there and you're pretty done.
Mime, Shuckle , and Spiritomb are your front liners in this deck, Q whichever one suits the deck you're up against and run with it. I like the dunsparse addition, as well as the Speed Stadium idea.
Perhaps running a couple of pokemon reversals might be just what the doctor ordered? Being able to pull up a specific creature that is a threat to your wall creature is excellent.
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It doesn't matter if Shuppet can 2HKO Machamp, because you can't play it down the same turn you fade it up, and you cant send it out the next turn because you can't play it from your hand to the active spot. That means it is out of the action for 2-3 turns just by attacking. And if you only have 1 benched pokemon, fade out, the next on is OHKO'd and its good game to you.
I'm not sure if you've caught this or not, but I guess I'll do this either for you or for anyone reading who's not familiar with the way shuppet plays.
You have a "wall" in the active spot, something with a single retreat cost. Generally this is Mr. Mime from the MT set (best bet is with mime JR under it which will completely shutdown takeout till you've got 3 energies on machamp).
Unown Q the wall. This way it's got free retreat (you can also typically play Moonlight Stadium if you wish as two of the 3 walls are Darkness/Psychic).
Each turn you drop shuppet to the bench, retreat the active for free, drop your trainers, damage your opponent and then scoop shuppet to your hand. Rince/repeat. I'm not sure why you are suggesting it's going to take 2 - 3 turns between shuppet attacks.
The largest threat here (other than Dialga G and trainer lock...which seems to go away if you play Shuckle as your wall since dialga almost always has special metals attached to it.) is a machamp built up to three energies on the bench. It's why my son and I are considering playing pokemon reversals in here (now that they're available), see what your opponent is trying to build up to break through your wall, bring it up and KO it as best you can.
Admittedly, you're going to have to work around take out, but given Machamp's weakness to Psychic, and the cards in format, I don't think it's a complete deck killer.