X? And Y? Their names somehow match the titles

That's how it is for all the story arcs in this series. If you look back at the rest of the Pokémon Special, you'll find the rest of the main characters are named after their respective games. Any remakes simply feature the characters named after the original games.

Yeah, just look at the very first manga with Red, Green, and Blue (Blue as the rival while Green is the girl in the english version).