"Mewtwo is basically uncounterable, bar stupid shit like SpDef Dark Arceus"
Yeah, but this is called Counter that Pokemon for a reason. If team 1 starts with Mewtwo, team 2's first pick will be a Mewtwo counter, such as Dark Arceus.
"This Palkia is a beast that can fake a Choice Scarf set"
I doubt it. The eventual battle will be with the teams listed in the OP; both players know the exact teams so no trying to fake something.