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I have 3 old games (and 1 new) names to help you, that really fit to the theme but in two very different ways:

-"Fahrenheit " a very interactive story where all your choice can matter (different endings). Some chapters, You play a murderer that try to hide that he is the murderer, and understand what happen to him. Some chapters, you play the cops that try to know who is the murderer. You really play the both sides. This game is a little crazy in his concept.

-"Lost Viking" (the ancestor of "Trine") is an platformer with reflection where all the 3 character are very different and need to cooperate, one can jump and run, one can fight with sword and bow, one can use shield to protect the other or to lift other with his shield or to glide with the shield. Character are multiple in all senses of the term. it's very fun, at almost each mistake in the enigmas one of your character die and all the tree guys need to reach the end, of course :). "Trine" is a modern game that is inspired by the same concept.

-"Gobliiins" is the same idea in an adventure game: one can use object (he's "more" clever), one is strong (he can try to lift or punch a lot of things), one use an unpredictable magic. It's very fun. my favourite adventure game of all time.

Multiple main characters does not mean that the characters need to be playable. It also does not mean that they both need to be protagonists. Just my 2 cents. Hope it helps.