First off, none of this really matters. Whatever you like, whatever floats your boat--fine. Go with it and the rest of the world be damned. Het, yuri, yaoi, no pairing at all--fabulous, my friend. Find your happiness where you can. That said, you can go on if you wish or skive off for better lands. After all, this is just one theory that can never actually be proven because Gundam Wing is more a myth that deals with humanity as a whole in its ability to adapt, not a squalid little "shoujo" story about "who loves whom."
This is a touchy topic for many members of the fandom, as they each have their own favorite couples (or larger groups) based upon their personal opinions of what goes on both in and outside of the television series. Both Emily and I have our reasons for supporting the featured formations in our fics, but the major thread running throughout is "plausibility within the constraints of the canon."
For clarity's sake, that means 1+2, 3+4, 5+Meiran, 6+Noin, and Relena +1 predominate.
1+2: Easy-going Duo clearly makes an impact on Heero, as is demonstrated in the adoption of his name as an alias. Given the choice of killing an obstacle or supporting a wounded comrade, Heero aides Duo's escape from the detention center. Merely paying back his debt from earlier in the series? Perhaps the baka has grown on him. Duo seems to easily create alliances/friendships with the other pilots quite quickly, even getting gruff Wufei to lower his defenses somewhat in their time as OZ prisoners.
3+4: The chemistry between friendless Quatre and lonely Trowa is evident from their first moment on-screen. Soft, warm moments are interspersed with anxiety and grief for each other. For more about the solitary nature of Quatre, please see the appropriate essay.
5+Meiran: From Wufei's Episode Zero Manga background, his devotion to his equally stubborn wife Shirin Meiran continues on into the series with his dubbing his only ally, his Gundam, Nataku. A Chinese warrior woman, this identity is associated with Meiran and is greatly revered by Wufei (his continued insistance throughout the series that he is unworthy/too weak to pilot the Gundam confirms this).
6+Noin: This may be a very one-sided relationship, as Noin is forever pulling her punches and diminishing herself to make Milliardo look the better soldier/leader/person of the two. A capable individual, Noin shows deep signs of affection toward the Sanc royal, trusting him implictly when others find fault with him. She follows his orders to protect Relena, leaving his side against her wishes. Milliardo's decision to fight her allies, the Gundam pilots, at the series' end saddens her, though she does not want to harm him or cause him to be injured in a scurmish against the pilots. For his part, Milliardo is confused and more apt to focus upon ideals such as honor, virtue and peace rather than the human aspects of life--the day-to-day problems and concerns of the ordinary man that Noin broods upon.
Relena+1: From the first moment she meets the mysterious Heero Yuy, Relena is attracted to the danger and uncertainty he represents. A strange boy who is like nothing she has experienced in her short life, Yuy becomes a bit of an obsession for the pampered girl. Though she does grow in the series to realize the wide-spread actions of war and the influences of political entities, the school-girl crush on the enigmatic soldier remains to create an affection that is reciprocated by Yuy as a tentative protector/shielded relationship.
These pairings are further supported within the individual fics by realistic exploration of characters and actions. If there is no seed, there will be no bloom. Out-of-character interpretations are allowed only in the humorous pieces to further a sense of levity. In a way, you can say that all humor is AU.
We pride ourselves in presenting dramatic stories that are believable in their conclusions and hope you can appreciate many fics on this site not for a sense of novelty, but because they are well-written and solidly constructed items of deep understanding.
Perhaps you can see these as strange suppliments to the canon... our way of looking at possible tiny threads at the frayed edges of a moving tale of war, peace and human frailty.