Can we settle that Kira loves both of them at seed?
the way Kira loses control and tries to save Fllay while Forbidden shoots the freedom's head off (but got to admit that the ultimate coordinator also plays a factor), the emotion Kira shows when he thinks he manages to save Fllay before the cursed dragoon from Rau, not to mention that Kira mistook Lacus as Fllay...
Kira loves Lacus, but he shows a lot more human emotion with Fllay....so as an audience, I would say Kira loves Lacus in seed, but he also has deep feeling with Fllay, then in destiny, well, Kira can devote 100% to Lacus since Fllay is a goner XD