I have an idea for Little Witch Academia/Godzilla crossover called: Godzilla X Little Witch Academia: The Two Worlds. Basically, this takes place several years after the events of the series and revolves around the daughters of Akko and Andrew, Sucy, Lotte and Frank, and Diana.
Ever since Atsuko "Akko" Kagari unlocked the Grand Triskellion, Magic is no longer a scarce resource for witches and has now become part of everyday life.
Among the new witches of Luna Nova Academy are Tsukina "Tsuki" Kagari, the daughter of Akko who is determined to step out of her mother's shadow. One day, during a dungeon run, Tsuki and her friends, Amelia and Kaari (the daughters of Diana and Sucy) come across a mysterious giant ring. However, that night, the ring reveals itself to be a portal as a creature steals a jewel from Luna Nova's vaults. Tsuki and her friends volunteer themselves to venture through the portal.
However, upon arrival, the girls find themselves on another Earth where humanity wages war with a race of giant monsters called "Kaiju", Godzilla chief among them. To make matters worse, the jewel stolen from Luna Nova contains the energy of a monstrous beast banished from their world. Now, the three girls must fend off a threat to both worlds, even if it means forging alliances with the most unlikeliest of sources.