From what I know, Superbot (the devs) were able to sit down and talk to Square Enix about including Cloud Strife in the game, but they apparently unable to agree on how he would play. --- PSN: snovvbub Sackboy main here.
Do you really think a company like SE would let Super Bot use their characters?
I know SE is a bit of a jerk these days to put it mildly, but I think they could have boosted some of their quotas by incorporating 1 character sure. Royalties aside, just adding your name brand into it makes people interested in your games/companies.
Unless the two companies are like mortal enemies or something.