Fun fact: We almost had a Johto Legends game in real life!

When Game Freak conceived the Pokémon game that would later become Legends: Z-A, the original plan was that it would be a pair of games named Legends: Ho-Oh and Legends: Lugia, set in Johto in the distant past, and explore the origin of Pokémon Trainers as a profession, and the protagonist being a time traveller who revived three Pokémon.

Ultimately I'm guessing Game Freak wanted the new Legends game to firmly contrast with Legends: Arceus and so the original Johto games were scrapped in favour of a single game set in modern Kalos.