I'm not really very knowledgeable on Final Fantasy. I just know that Cloud represents the Final Fantasy series when it dropped off of Nintendo platforms, and he has never been anything but cameos in games on Nintendo systems. And the number of those games he has made cameos in can easily be counted on one hand (Kingdom Hearts Chain of Memories, and two Theatrhythm games).
I know Cloud is very popular as a general gaming icon, but he has nothing to do with Nintendo, and I don't much care for this transformation of "third party characters are guests that have history with Nintendo" to "Any popular third party character", there are still so many amazing Nintendo characters to add, that it doesn't feel right to see that happen. If Black Mage is more of an icon for the early Final Fantasy games on Nintendo platforms, then that would be a more appropriate character. But alas, there's nothing that can be done now. I just hope that this time we get more exciting appropriate characters that actually have something to do with Nintendo... You know, like Isaac.