Wouldn't your request be better suited for this thread? http://thefanfictionforum.net/showthread.php?tid=18355
I can recommend a few, though I've only read one SEED/Destiny time travel fic, where after Destiny, the Strike Freedom is refitted to utilize the Voiture Lumiere without deploying the DRAGOON units. Shenanigans happen and the test to utilize the Voiture Lumiere causes him to go back in time to the JOSH-A battle, right when Rau steps outside carrying Flay.
Unfortunately, it didn't get much farther than that when I last read it. I'm not even sure what the name of it is anymore.
As for my other recommendations...
First, of course, there's
Fallen Angel, and it's sequel,
Soaring Above.
Fallen Angel takes place halfway through Destiny, right around the time of the Archangel's first intervention between Minerva and ORB. Basically, before Destiny, the EA had a program where they tried to, and eventually succeeded, in resurrecting slain people to create new Extendeds. The first, and only success, was Flay Allster. The story continues up through the end of Destiny, and has major changes to the events that occur. Very excellent read, but not for anyone who prefers Kira/Lacus.
Soaring Above takes place after Fallen Angel, and personally I don't find it as good as Fallen Angel but still decent. Follows Shinn and Cagalli, and to a lesser extent Kira, in the aftermath of the war in the previous fic. Can't really say much without spoiling what happens in Fallen Angel.
Another fic set is Enchanter468's series of stories:
Second Chance,
The Necklace, and
Gundam SEED: Evolution.
Second Chance depicts the end of Gundam SEED as it was, then continues it by having Flay's body recovered after the battle and successfully resuscitated. Kira and Flay have a reconciliation. Not for Kira/Lacus fans, again.
The Necklace is a oneshot that takes place between the three fics, detailing an event referenced in the next story. Not necessary to enjoy Evolution, but why not?
Gundam SEED: Evolution follows Second Chance and The Necklace, depicting an incident between SEED and Destiny where Coordinator radicals kidnap Kira so they can try and replicate the Ultimate Coordinator. An interesting read, detailing some necessary cooperation between the Archangel, ZAFT, and the EA (because it's way too soon after the first war and not even the EA wants it to start again yet). Sadly, it's incomplete, but still worth the read, I think. Kira/Flay again, but some Lacus in there and she was to play an important role. Also features some Destiny characters appearing (and not just as cameos). Should this EVER get completed, the author was going to follow up with a Destiny analogue story.
My next recommendation is
Saving Flay, a short what-if scenario that takes place in SEED, just after the revelation in Mendel (and before the battle ends). Also well-written, with interesting diverges from the canon. Again, not for Kira/Lacus fans. You're seeing a trend here.
This next one was an... interesting read, called
Mother and Son. Post-Destiny, with a twist: Cagalli went through with the wedding with Seiran completely. Cagalli even had a son! There's just one little complication there. Oddly enough, this is said to
not be for Athrun/Cagalli fans, and even more surprisingly, not for Kira/Lacus fans either (but not because of Flay, I promise!). Shinn/Luna fans are safe though. A very amusing read at times, but also a very serious read as well.
My next recommendation is
Mobile Suit Gundam SEED: Renaissance. Post-Destiny, and interestingly enough this was written
before Final Plus aired, and so keeps Shinn's characterization from before the memorial meeting with Kira at the end of the series, making for an interesting aftermath and new conflict story. Shinn is the main character: he has left Lunamaria, and ZAFT altogether, still torn up by the war and Stella's death. Trouble begins to brew, and someone like Stella has been located. Shinn is thus extended an offer to join Terminal to deal with the upcoming troubles, and despite everything accepts. Sadly, also incomplete. I think. It's been a while since I read it.
And my final recommendation is thus:
Respect Between Enemies. Unlike my previous links, this one features mostly original characters and their interactions with the canon cast, without changing things up for the main storyline of Gundam SEED. Starts at the JOSH-A battle, in which a Moebius Zero pilot finds herself shot down by a ZAFT ace, and due to the intervention of Kira, finds herself captured by him instead of killed outright. Follows a very interesting story path about genetics, pheromones, romance, politics, spirituality, and toxic ethics, showing an interesting, and otherwise-hardly-explored look at ZAFT culture and society, concerning what drove ZAFT to the point they were at, and what drove Durandal to his path. Also features a well-written look into Native American culture. Way, way better than it sounds. If you read nothing else of my recommendations, read this! You will not be disappointed, even with it being incomplete.
Also, it has a sequel of sorts, a crossover between Gundam SEED and Gundam Wing. I recommend that you avoid it. While well-written, it DOES contain a good deal of slash on the Wing side. And it's not slash for the sake of slash (well, at least not ENTIRELY for the sake of slash), and has an interesting, and very much alarming, plot significance to it. I don't like slash myself, though, and I won't recommend you read it.
