Why does Kira never kiss Lacus on the lips?

This is never confirmed but a common theory is due to Kira's relation with Flay

(*Spoilers* ahead for those who haven't seen SEED)

Flays death really showed to have an affect on Kira as he switched from his new found pacifistic fighting style when he acquired the Freedom to killing Rau Le Creuset. Also Kira was manipulated into sleeping with Flay, so this might also have affected his relationship with Lacus. This is seen as when he wakes up after learning the truth of his origin (the Ultimate Coordinator), Lacus is leaning over him,and he has a flashback of Flay leaning over him when they slept together causing him to tilt his head away from Lacus.

However with all this said, it is still strongly implied that Kira and Lacus love each other deeply and they prove to be one of the most solidified relationships in SEED and Destiny leaving little to no doubt concerning their relationship.