People wonder why Cloud made it in, and the answer is simple.
Cloud not only brings in money to Nintendo due to his large fanbase, but he's gotten people talking about Smash 4 again.
King K. Rool, the Inklings, Shovel Knight, Shantae, Issac and even other Final Fantasy characters like Black Mage, Cecil, and Terra are all safe choices. People would have seen them, shrugged their shoulders and thought they looked cool.
Cloud brought buzz to Smash 4, and the fact it, when your talking about JRPG heroes, there is nobody more iconic or famous then him. He is the Mario or Ryu of JRPGs.
This has nothing to do with relevance to Nintendo, its all about what makes people open their wallets and throw money at DLC. The characters that I listed like King K. Rool, and Shovel Knight have fanbases, but Cloud has an insanely large fanbase.
I think Cloud making it in is a great thing. It further reinforces the idea that Smash Bros is a who-who's All-Star fighting game for some of the industry's biggest icons.
Let me be blunt here, nobody outside of the fanbases who asked for them care about Shovel Knight, Shantae, King K. Rool, Issac, or even other Final Fantasy reps. They are just another set of characters in the roster.
Cloud has brought some insane hype to Smash 4, and the fact is, he prints money.
That is why he made it into the roster.