Assuming no flips, because then the answer is obvious, AlexanderTheAwesome got it mostly right. If both sides have Gardevoir DEX in play and one side has Vileplume BCR in play, Mewtwo vs Mewtwo (or something with a psychic weakness) leads to the most damage dealt. The problem with this technique is that you'll end up decking out before attaching all of your energy and that you prize six energy each. I think if you use a combination of Lysandre's Trump Card and Vs Seeker, along with having another Pokémon on both sides to get constantly knocked out so that each player can get prizes, you'll end up being able to attach all the energy if each player draws perfectly (would also require a float stone on each side so that Mewtwo can retreat to the other Pokémon so it can be knocked out, but the payoff is still worth it). You'd also use an Iris on the attacker's side because that adds 200 damage as opposed to the 160 added for each energy.
With all of that, you'd end up attaching 49 energy to one side, and 51 energy to the other, + the Iris on the attacking side, leading to (((49*2)+(51*2))*4*20)+200 which leads to a whopping 16200 damage. Someone correct me if I did my math wrong, sort of rushed through it.