remm said: Is there any explanation as to why those 4 protagonists are minor arcana?
I don't think there is one. Just that the tarot motifs belong to the Persona series, not SMT as a whole, and there were just enough Minor Arcana left to cover the Protagonists the artist chose to display (no Serph, no Aleph, no Hero, no Devil Summoner prior to Raidou...)
Astara said: That's awesome, too bad some character are missing and some other have "wrong" arcana (like aigis, she's in the aeon arcana in P3FES and P3P)
It depends. During the Journey in FES and P3P, Aigis' persona are Chariot arcana, even though her link is Aeon.
Shinji's in a similar situation. Castor's Hierophant... but his link is Moon in P3P.
Astara said: It's like a dual arcana or something ? I'm a little confused.
Not necessarily. These characters with Plot vs. S.Link Arcana simply represent different types of conflict. Beyond their own issues, in the greater scope of the plot, their Persona belong to one arcanum (for instance, Aigis is Chariot, which roughly stands for power and the use thereof, and Akihiko is Emperor which is basically an immature form of dominion.) But in terms of S.Links, which are the representations of their personal conflicts and how the Protagonist sees them, they have other issues to confront --like Aigis trying to understand what makes a human "human" and Akihiko growing up from his self-perceived indomitable attitude to actually attain such attitude.
It could be said that the Arcana the characters are listed as being in, here, are the ones that the characters' own personalities best represent. This is supported by the way their own Personae all come from the listed Arcana, as a Persona is representative of the owner's nature (except for the secondary Personae acquired by those who fit into The Fool and The World).
The Arcana that is strengthened by S. Links to a given character does not represent the character himself, but of the main character's relationship with them. Maxing an S. Link with a character who can use a Persona doesn't make their Persona any stronger, but it does make your character's Persona(s) stronger.