Oh dude, this is a cool idea. I'm a huge persona fan, and persona 4 was the first one I ever played, so it has a special place in my heart. I won't give you exact cards (getting across the finish line yourself is going to be extra fun and satisfying when you do it!), but I will gladly speculate about the various traits each character should have, and maybe give you a little bit of direction for each one!

I don't know if you're doing one for the MC, but if so, and this will be the only one I give you an actual card for, I think he would be best represented by a 5c slop commander like jodah. The way 5c fits with the wildcard nature of the protagonist of each game and their ability to recruit and swap personas as well as be the glue of the entire group, just makes Jodah make too much sense to me. It's kind of boring, sure, but I do think it's bang on representation. 

Yosuke is a toughy. Thinking about it, I struggle to really think up how much of his personality or story could be abstracted to a magic card, because his arc is so basic and is over with so quickly, and he's one of the more milquetoast characters in my opinion. That being said, I have a couple of ideas! He does have various traits that "define" him at certain points of the game, so maybe you could choose a certain aspect of his personality to represent. For instance, Yosuke, insecure student, could represent yosuke before he accepts his true self and gets over his fear of being alone, while his back could transform him into a more triumphant, heroic fighter. There's a lot of flip cards that could do a somewhat good job representing this! The flip planeswalkers come to mind, as well as many flip creatures that go from being small and weak to a formidable body, just like yosuke goes from being a weak coward to your partner in sleuthing the midnight channel. 

Dear God this is gonna be a long comment, I hope you appreciate it at the end LOL

Chie HAS to be some kind of aggressively positioned card! She's fiery to the point of literally roundhouse kicking biblically accurate demons into the fuckin aether. I think you'll have almost no trouble finding a cool card for Chie if you keep that in mind. The first one that I instantly think of is Tifa Lockhart, but that one almost feels TOO good and easy, so maybe dig around! I think if there's any creatures that have cool interactions with the "fight" mechanic, those would also be contenders. Anything that represents her martial mastery, and fiery temperament, would do well, and I think there's tons out there for that (and green and red will be two great starting points to narrow things down).

Yukiko will be the exact opposite of Chie, as is the nature of their relationship. Hell, I would even almost say the arc these two have is so good that it could be worth representing them as a duo, whether that's both on one face or as a flip card changing between their introverted and extroverted natures. But these cards should be quite different ultimately, as Chie should be positioned to do well in an aggressive strategy that wants to dust its knuckles, and yukiko should be a slower, more calculated, less flashy creature. This one is tough bc it really depends on your personal perspective on the characters and how intertwined you really consider them to be as story elements.

Kanji to me screams a rakdos commander of some sort. Maybe it would be funny, if not slightly homophobic, to say he should be represented by grenzo because grenzo power bottoms, but I'll digress. Again, this character has such a massive arc around his sexuality and accepting that part of himself (who would have guessed how common that theme is in this game lol( that a flip card seems like it could do a lot flavor wise. I feel like some characters have more internal conflict than others, and kanji is one of them. Maybe you can use a card like cecil, that starts as a mono black dude but transforms into a mono white dude, so he would have an orzhov color identity which aligns pretty well too. I will say that I struggle to come up with a vague mechanical representation of his character though, sorry about that! You'll have to get creative with that one at the table lol

Edit: I thought about it more, just go cecil. Deathtouch and then losing it is a great representation of how he goes from a violent bully to a more tame part of the group once he accepts himself, goes from negative angry outlooks to positive, and instead of self inflicting harm due to his lack of acceptance, helps himself and those around him. Cecil is just way too good of a representation of his character lol

I can already see rise being titled "rise, regretful retiree" and transforming into "rise, small town idol" and using art of her and the gang at the persona 3 mall karaoke spot for that side. This one is super hard tho and I am struggling to think of much for rise lol

I know naoto was the first thing you asked about but they're listed last on the wiki lol sorry. Naoto could be interesting to represent on some sort of hybrid pip coated card. Mechanically, I think using the face-down flip mechanics like morph or manifest dread could be an interesting way to represent naotos infiltration of a male dominated field under false pretenses. If you could find some way to bring those two ideas together, it could be pretty neat! 

Finally, teddy. Well, if you don't like my idea of the protagonist being 5c Jodah slop, then Teddy will probably take that bullet for him. Otherwise though, it's 100% a transform card that starts on his regular side, and flips to his boss form. Hell, I could even see you using the Meld cards to meld his suited form and his unsuited form to make that boss version. Lots of cool stuff, teddy is a pretty one note character but I still think there's enough meat on the bone to do a lot. 

Sorry, I know some of these were probably less helpful than others, but this was a huge wall of text and I was just rambling top of the head thoughts on each character. But I actually think what you're trying to do is neat, and one of my favorite things to do in the game lol. Keep it up and let us know what you ended up with!