And Kyon gets to see the reason Ayumu is so chill with Haruhi here... he has a miniature lookalike version living with him constantly.

Oh, I have another thought - there's a point where the girl who murdered Ayumu mind-alters Orito to make him think she's his childhood friend and get him to bring Ayumu to her. Later on Ayumu meets her and they end up in a big fight... We could work Kyon into figuring things out by either having him be the person who was altered instead, or if you think that shouldn't work on him, have him just be suspicious. Either way he could follow Ayumu and end up learning things that way.