The CEO of Level-5 took the idea to Capcom.
During the Level-5 Vision presentation for the newly announced Professor Layton vs. Ace Attorney, Akihiro Hino, CEO of Level-5, said that he was the one who initiated the exchange with Capcom for this particular title.
He did not expect a positive outcome, joking that that many people could be waiting for Ace Attorney 5. However, Shu Takumi, creator of the Ace Attorney series, was excited to work on a crossover title for the first time, after his initial surprise at the suggestion. Takumi is working closely with Level-5 on the title, taking charge writing the scenarios.
So far, we know that this unexpected match-up will be set in Labyrinth City, a strange world that Layton and Wright find themselves in together. In this world, illusions and reality coexist, witches live in the shadows, magic is real, and the city is under control of the Story Teller, a villan whose writings become reality and control the future of the world. Due to the increasing number of impossible happenings in the town, Professor Layton will of course find himself facing new puzzles, while Phoenix Wright finds himself defending someone accused of witchcraft.
The Japanese website for the game opened today, showing a book titled "Witch Trial" with pages featuring the trailer for the game, screenshots, and trailers for the Japanese versions of Phoenix Wright: Ace Attorney and Professor Layton and the Specter's Flute. The background music provides a small preview of what we might expect from the combination of the two series.