The Truth, the whole Truth and nothing but the Truth!
It's been confirmed that Athrun and Cagalli DID NOT SEPARATE. Athrun did NOT get together with Meyrin! This is official!
The creator of Gundam Seed and Gundam Seed Destiny, Mitsuo Fukuda, made an appearance on television apologizing for not making it clear that Athrun had returned to Cagalli at the end, he was even wearing an Orb Admiral uniform.
Besides, interview with Naomi Shindou (who voiced "Cagalli Yula Athha") said: "... However, according to the director (Mitsuo Fukuda), he said that was the speech from the representative head's standpoint. Cagalli approaching Meyrin "Please take care of Athrun", for Meyrin, it was "You will be fine to get on the Archangel". It seems Cagalli, as the representative head, helped Meyrin by providing her a place to stay, isn't it?"
The director of the show, Mitsuo Fukuda, then created two AMC's (anime music clips) where he made this clear to fans who had missed the airing of this report. The two AMC's are known as 'Reason' and 'Akatsuki no Kuruma'. Their authenticity is proven towards the end with Fukuda's signature and Sunrise's approval.
Reason (I so love this one!)
Akatsuki No Kuruma (this one is a little cheesy because of the flowers but it has Fukuda's signature at the end which proves that he made it, so put the blame on him.)
Source: Director's Concept Gundam Seed & Seed Destiny AMC (anime music clip) Perfect Collection. Bandai Channel
By the way, I'd like to clarify that these are NOT AMVs (Anime Music Videos) but AMCs (Anime Music Clips), there's a difference! These are NOT fan-made, though they were uploaded by a fan. But if you still doubt the authenticity of these videos and the AsuCaga happy ending then, I suggest you read the forum on this link, especially those that are written in RED, posted by boredandsleepy, the same person who uploaded these videos on youtube.
Animesuki Forum
If you still have questions just sent me a message, I'd be glad to clarify anything else, as long as my brain would let me.
AsuCaga ended up together!
Spread the word people!
Thank you!
AsuCaga FOREVER! ♥