Definately Kira and Lacus. They are very popular couple in Japan. From what i heard, They were ranked #1 in March,
2004, which is a pretty big compliment considering how many couples there are. In the show, their relationship
isn't developed or as bluntly stated as other pairings, which is probably why they aren't as popular in North
America. However, that doesn't make them a worse couple, they're just harder to understand and analyse.
Lacus, in essence, is much like Kira's healer. She's the only one in the show that seems to be able to comfort
him properly. When Kira was badly injured after a battle with Athrun, Lacus is the one that found him and gives him a
nice retreat to heal. While his injuries were recovered, Lacus provides him with a place to heal mentally as well. Lacus
is like Kira's guiding light. She helps him numerous times along the way and is always there for him. She's
one of the few characters that haven't betrayed him or used him for some other means. While Kira is constantly
protecting others, Lacus gives him a break when she protects him. Also, the one time Lacus shows some sadness, who does
she go to for comfort? Kira of course. Lacus always seems to have this serene mask on, but she finally drops it when she
mourns for her father's death with Kira. It's evident that she has feelings for him. She's willing to
sacrifice everything to help him. Their relationship is more evident in Gundam Seed Destiny. They seem to know each
other a lot better then. One glance at each other, and they'll know that something's troubling them. It's
like they have a silent communication. And they always have only the best intentions for one another.
Lastly, Kira goes into battle again in order to protect her. He hates to fight, but I believe with some healing from
Lacus, he's finally able to conquer his demons. Really, what more can I say? They have a mature relationship and
it's clear that they care for each other very much. They understand each other and are able to help and comfort one
another through a dark time.