Some of the last few sets have been based on Mega Gengar, Fighting types, Charizards, or Gold-coloured Zoroarks. The TCG is only tangentially marketing the main games, and they'll profit off anything they choose to print. Plus TCG expansions are usually based off multiple Pokémon at once anyway, with incomprehensible levels of relevance (one booster art gets Groudon, another might get Houndoom, or whatever).
Edit: just checked. Zygarde' set is themed on Psychic Pokémon, with BREAK Pokémon and Zygarde as secondary themes. It had to release some time, anyway, the been even a regular Zygarde card yet.