I'm not entirely sure. You have to have some reason to play them. I think TPCI is keeping that in mind, what with both of the non-EX Pokémon not being very special.
Azumarill hits Fire- and Dragon-types for Weakness. Neither of these types are super prevalent in the meta game as of now (although following the release of Volcanion-EX they certainly could end up so, or perhaps the more recent Delphox).
Shiftry takes down a sub-type of Psychic and a sub-type of Water. A lot of popular Water-type Pokémon are weak to Grass as of now, so that's a bonus and a definite counter to Greninja BREAK, but most Psychic-types in general are weak to Psychic instead of Dark, such as Alakazam-EX and Wobbufett. Shiftry could certainly be a good, strong counter against Night March, and both of the decks he'd be useful against are in a serious need of a solid counter.
Volcanion-EX is also not that overpowered in terms of weakness, only really dealing with threats like Vespiquen and Vileplume.
I'd say your best piece if evidence would be Mega Gardevoir-EX. Not only is this card broken to begin with, especially in Expanded, but it also swings for weakness against things like M Alakazam-EX, Lucario-EX, and such things.
But all that being said, I still totally see what you're saying, and all of my evidence is very case-specific so it could certainly be made null by the next reveal (if they released some sort of Fighting/Psychic-type?).
Cheers!