Short answer: Lacus Clyne chose Kira Yamato because they are both alike. They both share the same goal and their personalities match. Even though there is a significant lack of romance between Kira Yamato and Lacus Clyne in Gundam SEED and Gundam SEED Destiny, there are scenes where affection or fondness is shown.
Lacus Clyne is one of the lead females in Gundam SEED and Gundam SEED Destiny. She was introduced early in the anime/manga and as the story developed so did her character.
In terms of development towards a romantic partner, we first have to talk a little about Lacus Clyne a bit and then also talk about her romantic partners. We are talking of course about Kira Yamato and Athrun Zala.
She first appears after Kira Yamato saves her from a drifting life pod in space. We then learn that she is Athrun Zala’s fiancée and that she is the daughter of PLANT Supreme Council Chairman Siegel Clyne. Being the daughter of the Chairman of the PLANT Supreme Chairman, she herself, with her songs and words, has a great deal of influence over the people of the PLANTs.
Gilbert Durandal, PLANT Supreme Chairman during the second Alliance-PLANT war, even stated that her influence is far greater than his during a meeting with Athrun Zala.
Bearing the family name of Clyne, Lacus has been shown to have a lot of access to Military bases and Hangers. Examples of the power she gains from her name, words and songs can be seen when she gives The Freedom to Kira Yamato. One of the most powerful Mobile Suits in Gundam SEED.
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In Gundam SEED, the PLANT Supreme Chairman, Patrick Zala claimed that Coordinators are a new species, and that the only way to stop the war was to eliminate all the naturals. Lacus Clyne’s belief was different. She did not see Coordinators as an evolved species. She saw Coordinators and Naturals as the same thing, Human beings. She instead talks about building a better future in peace with the Earth and especially in that PLANTs where the birthrate is declining.
After the death of her father, Lacus Clyne has kept to her belief that the war will solve nothing. She stands firmly on her belief that Naturals and Coordinators can live together in peace.
Background with Lacus Clyne
During Gundam SEED, Athrun was engaged to Lacus Clyne as it was seen as favourable for the PLANTs that the daughter of the PLANT Supreme Council Chairman and the son of the National Defence Committee Chairman be married. Due to his duties for ZAFT, Athrun never spent much time with Lacus and later on was no longer engaged to her due to her being charged of treason as well as her propaganda of peace.
It can be seen in many scenes with Lacus and Athrun that Lacus has a great influence on Athrun and that Athrun deeply cares for Lacus.
Other romantic interests
Cagalli Yula Athha
Although Athrun Zala is the fiancé of Lacus Clyne, when the Clyne family started their propaganda about peace between Naturals and Coordinators, his engagement with Lacus Clyne was ended. Later in Gundam SEED, Athrun meets Cagalli Yula Athha, the daughter of the lion of Orb and later the Cheif Representative of Orb.
Like Athrun, Cagalli Yula Athha has a strong stand for loyalty and respect.
In the later parts of Gundam SEED the Athrun and Cagalli start to develop feelings for each other, and although it was never mentioned, it can be seen in Gundam SEED and Gundam SEED Destiny that the two have mutual feelings for each other and that they begin to date.
She is a red coat mobile suit pilot for the Minerva and is a supporting character of the show that every now and then casually flirts with Athrun Zala. However, when Athrun meets her in Gundam SEED Destiny, he is already in a relationship with Cagalli Yula Athha.
Athrun, however, does not seem to show any romantic interest in Lunamaria. This often leaves her with a pout on her face but it does not stop her from trying to flirt with him again another time.
She is the CIC of the Minerva and the sister of Lunamaria Hawke. Unlike her sister, she did not try to flirt with Athrun Zala. However, when Athrun was being pursued by ZAFT under the charge of treason, she helped him, and escaped along with him.
In the special ending of Gundam SEED Destiny, we can see that it is Meyrin who is with Athrun, not Cagalli, when they visit the memorial at Orb, but in the last scene of that episode, Athrun is wearing an Orb uniform again, telling us that he returned to Orb, back to Cagalli.
The creator of Gundam SEED, Chiaki Morosawa, also stated that Athrun Zala ends up with Cagalli Yula Athha.
In the early parts of Gundam SEED and Gundam SEED Destiny, Athrun Zala shows that he believes in ZAFT and the words of both Chairmen at each time. Later on though, his beliefs align with those of Kira and Lacus, and later in Gundam SEED Destiny, he tries to make Shinn Asuka understand his view on the war. During his time with ZAFT in Gundam SEED Destiny, his skills as a Mobile Suit pilot was recognized as he was made a member of F.A.I.T.H. which makes sense because in Gundam SEED and Gundam SEED Destiny, Athrun Zala is one of the best Mobile Suit pilots.
Background with Lacus Clyne
He first meets lacus when he rescues her from a drifting life pod in space, and since then the two have shared a fondness for each other. While she was on the Archangel, Kira would often show her kindness by giving her food and being with her.
In Gundam SEED Destiny, we see them living together, along with reverend Malchio and many children before it was attacked by ZAFT.
Lacus Clyne has always been able to comfort the saddened heart of Kira Yamato. Kira, being emotional as he is, vents his frustrations and sadness in Lacus.
However, throughout Gundam SEED and Gundam SEED Destiny, Kira has never really shown affection for Lacus. It is always Lacus who shows affection, like a hug. The most affectionate thing that Kira has done for Lacus is give her a kiss on the cheek when Lacus gives Kira the Freedom.
In the early episodes of Gundam SEED, Kira Yamato can be seen as a young teenager who does not have a political view of the war and just wants to live in a peace in the neutral territory. All of this changed when he meets his childhood friend again, Athrun Zala, as well as a Coordinator named Lacus Clyne.
When he meets Athrun again, he is fighting with the Earth forces to protect his friends while Athrun is with ZAFT. This throws Kira into a dilemma… does he have to kill his friend? What is the point of all this fighting anyway? He goes on to question
and then Kira meets Lacus Clyne, who gives him the idea of not fighting for one side, but for fighting for what you believe in.
Although he did not leave the Archangel, the Kira Yamato that came back to Earth after being healed by Lacus Clyne in the PLANTs, decided that he was no longer with the Earth Forces.
Just like Lacus and Athrun, Kira believes that Naturals and Coordinators can live together in peace. In Gundam SEED Destiny, he continues to stand by this belief by intervening in battles among ZAFT and the Earth Alliance.
Other romantic interests
She is a Natural and is the first romantic interest of Kira Yamato in Gundam SEED. In the early episodes of Gundam SEED, she is engaged with Archangel Crewman Sai Argyle. This leaves Kira Yamato a bit depressed but still clinging to her.
Just like Lacus Clyne, Flay Allster has always been able to comfort Kira Yamato when he feels down.
Flay later realizes that Kira has feelings for her and uses them to manipulate him. She constantly hugs him and kisses him as he cries. She even goes as far as having sex with him just to manipulate him.
It cannot be emphasized enough that for Kira, Flay Allster was important as he was in love with her.
In the last part of Gundam SEED, she dies from the hands of Rau Le Creuset.
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Our Final Thoughts
So why did Lacus chose Kira and not Athrun?
She probably felt that she and Kira are kindred souls, because of them having many similar traits and beliefs. This similarity made her fond of Kira and that later gave fruit to love.
It is quite weird though that she loses her feelings for Athrun so fast, or perhaps she never really had any feelings for him in the first place as their marriage was arranged.
During an interview with the author of Gundam SEED and Gundam SEED Destiny, Chiaki Morosawa, it was revealed that Kira Yamato never really loved Lacus Clyne. Perhaps it was because he never really moved on from Flay.
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