How can you forget Lucian vs Thresh?
Aatrox has s special interaction when he sees an enemy Tryndamere.
Caitlyn and Vi have a special "buff" which stacks every time they kill/assist against Jinx, and vice-versa. They MIGHT also gain 1 bonus gold per kill/assist, but I don't remember if that is correct.
Miss Fortune and Gangplank have special "buffs" about being a Pirate Hunter and Pirate respectively, but they do not interact like the above example.
Shen, Zed, Akali and Kennen have a special "buff" that simply states that they are a ninja. Additionally, if there are 2 or more of those champions on the same team they deal 1 less damage because ninjas are strongest when they work alone.
Aside from these there are many hidden interactions between champions aside from secret taunts, including such things as bonus gold every time Zyra kills Sion and vice-versa as a nod to Plants vs Zombies, Zyra's champion model grows when she is affected by Leona's Sunlight debuff, etc. It's not that they aren't there, they just aren't as prevalent as with Rengar and Kha'Zix, and for the most part they don't affect gameplay itself. I do feel we should have more "game changing" events like The Hunt is On though.