It really isn't that difficult to understand. The clues are there but because of their subtly and aloof undertones, it's easy to miss them unless you are actively routing for the pairing.
1). They were both outsiders and eventually came to understand one another.
2). Lelouch was only able to fulfill his goals because of the geass that C.C. gave him in episode one. Towards the end of R2, she asks if he hated her for ruining his life, and instead he thanked her for all she'd done for him. Their touching moment was conveniently ruined by Kallen's kool-aid man style ****block.
3). Lulu goes to C.C.'s rescue after Mao attempts to blackmail them. Later Lulu reassures her that he will stay on as her 'partner' and fulfill the contract that Mao couldn't. (Note: Remember that C.C. admits to loving Mao just before she kills him).
4). Lelouch not only learns C.C.'s real name, but discovers just how tragic her life has been, which further allows him to empathize with her position and intentions. Likewise, the reverse is true and because C.C. actively played a role in shaping Lelouch's past, she can understand his desire to pursue his goals.
5). After taking over as emperor and putting his final plan into action, C.C. understood his true intentions with the zero requiem. It wasn't that he didn't trust Kallen, but rather he knew she was better off not knowing. He knew how much Kallen cared about him but was thinking long term and knew he couldn't save the world AND be together with her at the same time.
6). Lelouch promised to make C.C.'s true wish a reality. Her deepest desire was not to die, but to be loved. This last one is the biggest kicker, because it's basically Lulu saying "I love you" without actually saying it.
They are my favorite pairing, and given my fondness of the series in general, it was very easy for me to pick up on everything that was going on between them.
Kallen earned the title Q1 because of her abilities. The queen is the most powerful piece in chess, and in Lelu's mind, Kallen was the most powerful companion he had. Giving her that code name had nothing to do with personal fondness. She simply had all the skills needed to make his plans come to fruition. Her strong determination to change the world (for her mother) and because she was an ace knightmare pilot. C.C. on the other hand was more or less the adviser/observer, which was more fitting because she was so detached from the events of human life (because of her immortality).
Also recall that the Black Knights joked that she was Zero's lover.
Lastly, yes Lelouch technically loved Shirley and even went as far as trying to get revenge for her death. He also admitted to loving Euphie before she died. And the undertones with Suzaku, while not my preference, are also very easy to spot, especially during the scene where Lulu dies.
But ultimately it's C.C. because of the reasons stated above. She is the one responsible for everything that happened and if they had never met, there would not have been a Code Geass.