The third season was darked than the two previous one. And contrary to the previous seasons' finales, not all the questions are answered before the cliff hanger appears.
The darker tone of the 3rd season may be the explanation of the decreasing audience. As teens are growing up, the Tragger family structure may evolve. And Kyle has much less things to discover from our world, as he did during the 1st season, and that was really funny.
This 3rd season was clearly planned with a 4th in mind: so many new characters, so many new unexplained connections... But definitively, Kyle XY deserves a more comprehensive and elaborate finale. Why not a last special episode to bring explanations and put an end?