I think we are all forgetting how Square operates, they operate based on which character makes them the most revenue. They have worked with Platinum games to put 2B in Soul Calibur 6, despite having to deal with another company. We have to keep in mind in order for this to happen Bandai Namco had to deal with both Square and Platinum Games. This is a similar situation many of the S-E characters in question are in.
Also lets count how many times Square has cross promoted FF. 1) Cloud Smash Wii U, 2) Ardyn & Bahamut Assasins Creed Origins, 3) Noctis Tekken 7, 4) Behemoth Monster Hunter World
Out of all the recent cross promotions the only one that isn't FF related is 2B is Soul Calibur 6. That really says a lot on how the company operates. They choose constantly to push their most popular and most profitable franchise. This is not a coincidence and the fact they allowed 2B in Soul Calibur 6 is not either. 2B was one of the most fan requested characters for Soul Calibur, Square saw this and noticed they could cross promote off of her and so they put her in. Yes it did appease the fans, but more importantly it gave something in return to Square Enix the thing they love so much, cross promotion. You might say well Cloud did not cross promote, and Sakurai chose him not Square. To that you are correct, to an extent. When commenting which Square characters they might have chosen Sakurai mentions Terra and Bartz. Nomura states Strago would be good too, this is yet another FF character. Sakurai then mentions Fusuya, all of these characters mentioned are FF characters, they are not from Square's lesser known properties. So keep in mind Sakurai chose the FF character, this does not mean he chose Cloud from a General list of Square characters. He was allowed to choose an FF character and thats that. We see through this Square sets parameters on who can be chosen, and they are related to areas they can cross promote. Also yes Cloud did cross promote, he cross promoted the FF franchise and FF14 that was released since 2010 and has had expansions to the our current date. Also FF15 would be released less than one year later after Cloud's release date.
We can see in all these business patterns, Square thinks ahead. They find ways to make the most money, and they will jump through hoops if its means they will make more money.