I don't think you're accurately representing the ZekEels side. For every Black Belt the Terrakion deck needs, the Mewtwo deck needs an Eviolite.
Plus you're simply not going to hit six PlusPowers over the course of the game, so you need four energy. But the Terrakion deck can use Eviolite, too, which makes it five energy. Plus, if you start OHKOing one every turn, they'll be doing 90 for 2, not for 3. So then it becomes six energy, occasionally five. Not an easy number to get on three different cards over the course of a game. A smart player will place their Eviolites and energy in a way that forces you to put six energy on each Mewtwo. Most Terrakion decks are also running Lost Remover now, which means you kinda have to set Eels up. But they're just easy prizes for Terrakion, and once they're gone, you're in trouble again since you probably don't have 15-18 energy in your deck, even counting DCE. Also, last time I checked, most Eel decks don't even run three Mewtwo although I can understand wanting three in some builds.
I find it kind of ridiculous people actually think a deck designed to hard counter ZekEels can lose consistently to the deck it's designed to beat yet still do well in various tournaments despite being incredibly under-played.
You still have to answer the burning question: why doesn't Terrakion run Mewtwo when it can fit it in so easily? Are the Terrakion players just stupid and want to auto-lose to any deck with Mewtwo, or can they handle the card without their own Mewtwos? Take your pick.