First, in protagonist the meaning of the prefix "pro-" is primary. It implies nothing about the character's nature except that they are the most important character to the narrative. The protagonist of a story can be the villain in moral terms (an antihero). Similarly, antagonist only implies that the character(s) who fulfills such a role is in opposition to the protagonist.
Second, Riku is not an antihero. He is temporarily allied with an antagonist, but he is being manipulated. Riku's storyline follows the prototypical hero's journey more closely than Sora's as he experiences the essential phases of revelation and atonement in a way that Sora does not (finding out that he has been manipulated and then turning to help Sora). He is the best candidate for deuteragonist, if there is one.
As for the OP's question, the idea of a trinity of protagonist, deuteragonist, and tritagonist is irrelevant in the discussion of an ensemble cast. There is a reason that the terms deuteragonist and tritagonist are very uncommon outside of discussion of classical Greek theater (in which the roles were played by three actors who were assigned the roles of protagonist, deuteragonist, and tritagonist). Kingdom Hearts has a far too vast and varied cast of narratively crucial characters to try and shoehorn them into these three roles.




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