Smashboards

Final Fantasy as a whole has made a huge impact on Nintendo, and Cloud's the most popular (or at least the best-known) character by far. If any other Final Fantasy character was added, plenty of people would be asking "why didn't they include Cloud?"

https://sourcegaming.info/2016/01/20/sakurai-x-nomura-creator-interview-2016-part-one/
https://sourcegaming.info/2016/02/23/nintendo-dream-interview-with-sakurai-part-2/

I'm not familiar with Shin Megami Tensei or Persona, so I'm not as sure about that (I've only played Persona 4 and 5) - I know that Persona 5's user interface inspired the UI for Smash Ultimate. Sakurai really enjoyed Persona 5, he doesn't care about the console wars (as he stated in the second interview that I linked above), Persona 5 gathered a ton of acclaim from critics and fans alike, and I'd imagine that Sega already being involved in Smash would help.

https://personacentral.com/atlus-interview-joker-smash-p3-p4-projects-future/

It doesn't have to have a connection to Nintendo either. Smash has now become a celebration of Video games. Take Pac-Man, I don't think he has much to do with Nintendo however his impact on Gaming is obvious

Like Megadoomer said, Final Fantasy has been a huge franchise for Nintendo spanning multiple generations, with the first six games being some of the most famous JRPGs on the Famicom/Super Famicom, and numerous spin offs and ports being released on GBA/DS/3DS/GC/Wii/etc. Final Fantasy has also made direct crossovers with Mario, like Mario Hoops 3 on 3 and Mario Sports Mix, as well as many homages to Final Fantasy being featured in Square and Nintendo's collaborative game Super Mario RPG. Cloud just happened to be the most popular character so they chose him.

Shin Megami Tensei has also has a long history with Nintendo stretching all the way back to the Super Famicom to SMT V being one of the first games announced for the Switch. Persona has also had its spinoff series Persona Q2 featured on the 3DS, and SMT, like Final Fantasy, has also made direct crossovers with a first party Nintendo IP, being Tokyo Mirage Sessions Fire Emblem. Joker also happened to be the most popular/relevant character from his series like Cloud so he was chosen.

MajoraMoon Pac-Man has had plenty of games on Nintendo consoles, Miyamoto has mentioned Pac-Man being his favorite video game character (he directly stated he likes Pac-Man more than Mario), and Pac-Man has crossovered with Mario before in the Mario Kart Arcade GP games. Namco Bandai themselves also happen to be the developers of Smash 4 and Ultimate.

Huh, really? The more you know

That's why their inclusion is so great! Don't limit yourself to one console manufacturer. I'd love more PlayStation and Xbox reps.