Metal Gear on NES... Metal Gear Solid Twin Snakes on GameCube... Metal Gear Solid 3 on 3DS...
Cloud was never on a Nintendo console besides Final Fantasy Theatrhythm but I haven't seen anyone complain about him.
Besides Joker in Smash is most likely a huge hint that Persona 5 is going to be ported to the Switch since the Switch is selling like Hotcakes, Atlus might want in and port it. I mean Joker DID appear as a main character in Persona Q2... which other than the cartoony artstyle still has a "M" rating.
Trust me. The "complaint" is there for me on Cloud as well. But think about this:
Sonic the Hedgehog is probably the BIGGEST culprit here. SEGA and Nintendo once upon a time were going face to face for awhile in brutal competitive action. Never would you see a Sonic game on Nintendo and even though that was over 15 years ago, look at him in Brawl and etc. Cloud isn't even a competitor. (Or in this case for Sonic, WAS) Just an unrelated piece of video game content. Again, I base which characters would be well on a bunch of factors. One of the factors being "video game icon". Cloud is certainly one of these as well as not being "Exclusive" to any system. Cloud not being on Nintendo was probably just a marketing thing where they felt they would not make as much money, who knows. It is very hard, FAR HARDER to justify Cloud than Snake, but at least those are icons... Joker isn't. XD