What if Marlene and Riley was mother and daughter?
What if Ish was the man with the family that try to catch a ride at the beginning of the game?
What if Ish and his people were hiding in the suburbs and left when Joel was taking care of the Infected and Survival ?
I doubt Riley was Marlene's daughter. Marlene knew Ellie since she was born, and Ellie only met Riley during the first comic (probably 3-4 weeks before Joel first meets Ellie.) If Riley was Marlene's daughter, Ellie would have had to know about her before they first met in the comic.
Also, why would the military let the Fireflies' leader's daughter in their boarding school?