There are several ways short plays with two characters can be constructed.
-- The most obvious is that they emphasize the main character, the impact character, and their relationship, with a functional nod to the Overall Story throughline. This would seem like a character driven piece.
-- Alternatively, the play may focus on one throughline heavily and include (or not) one or more of the remaining throughilnes, such as a play about a single character, or about a relationship.
-- Less likely is a play that focuses on the Overall Story throughline, the throughline where the objective characters interact. I say this is unlikely for several reasons:
1 ) One of theater's strengths is the audience acceptance of getting inside a character's head, whether it be through monologue, "internal dialogue," or other techniques. The OS throughline's objectivity doesn't allow for getting inside a character's head.
2) Another of theater's strengths comes from its intimacy and immediacy with the audience, something the Overall Story throughline lacks.
3) One of live theaters' weaknesses is the cost to do "big picture" storytelling. Very often plays are set in single locations, or use imaginative devices for 'creating' large or varied landscapes.
So, IF you are doing a play that has a significant Overall Story throughilne, and it is truly only two characters (as opposed to two players each playing multiple characters), then you might either choose to:
-- Make those two characters very complex, e.g. give each character one side of the dynamic pair and the other character the other dynamic pair characteristic, or...
-- Go simple and limit the number of characters explored, e.g. the protagonist and the antagonist, or guardian and contagonist, etc.