I can understand square/enix, the developers of this "fan-sequel" tried to get fame for doing another chrono trigger. Chrono Trigger is a brand, it was probably the most famous rpg on the snes. Square build up this brand, why should they let somebody else make use of it? The creators of the chrono sequel could have also made their own rpg, but probably noone would care, so they make a rpg in the chrono trigger scenario, so they get world famous for doing the chronotrigger sequel. You know if you want to make a game related to a film, like batman, you also need to pay the licence holders of batman money, for creating a game with the tag "batman". And above else this game could also be a bad game and would damage the brand then, which would lead to less income for square, which square needs to be able to exist.