If you ask me, I think the skill and power could break down roughly like this. Thoughts? And feel free to comment on any pilots I left out.
(Yeah, I did include some notable pilots that didn't fly Gundams...thought it would be fun!)
G Gundam Tier
Yes, these guys deserve their own tier. These are super fighters piloting super robots that are about as far from real robot as you get, to me it's pointless to compare them against the rest.
Domon
Master Asia
Schwartz
The Shuffle Alliance (both Domon's frienRAB and the originals) and Allenby
Urube (I believe he loses once, then kicks everyone's butt thanks to an amazing Gundam and DG cells, then loses)
C'mon, please don't ask me to rank the secondary fighters too. I don't know!
Comments: I say Domon is above Master. This is logical, not disrespectful to Master's greatness. In the end Domon did defeat him, the student naturally surpassed the teacher. And let's not forget that even before the final epic showdown Domon was occasionally able to take on Master with Shining.
I realize I might be slightly overrating Schwartz. But he's strong, and I think he's awesome in general.
The "GWO Doesn't Know Enough To Rank These And Will Leave Suggestions To Others" Tier
Usso and Katejina (Victory)
Loran and Gym (Turn A)
Garrod and Jamil + whatever rivals they had (X)
Ultimate Tier
(the very best of the best)
Amuro Ray (Char's Counterattack/MSG/Zeta)
Ribbons Almark (00)
Setsuna F. Seiei (00)
Kira Yamato (Seed)
Shinn Asuka ("berserker" only) (GSD)
Char Aznable (Char's Counterattack/MSG/Zeta)
Comments: These are the guys that are talented enough to be practically considered more than human more often than not. The tricky part here is how a true Newtype really compares against, say, a "true Innovator" or a top-notch coordinator. Though avoiding bias entirely may be impossible, I give the slight nod to Newtypes since it is theoretically the most natural state of existence. Innovation is a tougher process that is helped along by GN particles. It also takes an excess of particles to achieve the highest state of Innovator consciousness, but the psychic powers of a developed Newtype are seemingly always there.
I think coordinators are a step below Newtypes and Innovation, with the Zero system beneath that. At the end of the day Coordinators are extremely advanced physically, and that's the end of it. The Zero System makes you the perfect warrior--if you can take it. Wing's writing doesn't do much to endorse it either, and I agree with the many criticisms made of it.
At his best, Amuro seems able to take on all comers. And look, this guy helped deflect Axis with some help from Nu Gundam. You can make the case that others could beat him in a head-on fight and that might be true, but if we put hardware aside I just find it really hard to beat Amuro. Next is Ribbons, who managed to give everyone trouble even though his machine was likely about equal with 00 Raiser at best. Personally I think Setsuna is slightly more skilled and could beat hm with zero outside interference, but the final episode is what we have to go on and I can see the argument for putting Ribbons just barely above him.
Kira at full potential just murders everyone, that was true even when he was in Strike. I put Shinn's note there because at his absolute best he was better than Kira, but for one reason or another he hit this level only very rarely.
Char is arguably only high tier, but even in Char's Counterattack he can fight Amuro evenly despite not being, if memory serves, the most powerful Newtype out there by any means. In terms of pure skill, Char is surely excellent.
High Tier
Judau? (ZZ)
Scirocco (Zeta)
Kamille (Zeta)
Haman (Zeta/ZZ)
Zechs (Wing)
Heero (Wing)
Graham (00)
Ali Al Saachez (00)
All Innovators besides Ribbons (00)
Wufei (Wing)
Lockon Stratos (Lyle) (00)
Anavel Gato (0083)
Rau (Seed)
Comments: Given his defeat of Haman and the apparent info of Judau possibly being the strongest Newtype in the UC, his placement seems reasonable. Scirocco was exceptionally dangerous, and when you get down to it Kamille needed a desperation move to finish him off. To his credit Kamille was fighting in an arguably inferior machine (really, The O was a monster), so I do think he's close or roughly equal to him. Haman was perfectly capable of taking on Char and Kamille and as I understand it she puts up good resistance against Judau, and she's a Newtype.
Rounding out the bottom half we have Zechs and Heero, with a slight nod to Zechs for what he did with the Tallgeese and his successful attempt to fight four Gundams with only Epyon and a handful of grunts. Zechs might be inspired by Char, but he does take after the Red Comet. By the end he and Heero are probably about equal, though.
Graham? This guy could give Gundams trouble in a mere Flag. No outright victories, but his ability to survive despite a massive technology gap is amazing. Wufei is highly debatable, but this guy was a vicious fighter in Gundam Wing and definitely one of the most aggressive pilots in the franchise. I wouldn't want him as an enemy. Finally we have Anavel Gato, who wreaked havoc throughout 0083. I also agree that he had to overcome a tech gap of his own, at least until he got out of the unit 2.
It's a bit of a generalization to put all the Innovators on the same level, but they give Celestial Being enough trouble that it didn't seem quite right to put them in middle tier. Lyle makes high since in the final battle he had not one, but two very narrow victories despite the odRAB. Way to go. Rau barely makes high tier because of how much trouble he gave Freedom in Gundam Seed 50.
Middle Tier
Norris and Raraba Ral (8th Team / MSG)
Lockon Stratos (Neil) (00)
Alleujah (00)
Yzak (Seed)
Shani / Clotho / Orga (Seed)
Seabrook (F91)
Athrun (Seed)
Duo (Wing)
Dearka (Seed)
Cecily (F91)
Mwu (Seed)
Iron Mask (F91)
Tieria (00)
Rey Za Burrel (Seed)
Quatre (Wing)
Shinn Asuka (normal state) (GSD)
Cagalli (Seed)
Trowa (Wing)
Kou (0083)
Stellar / Aeul / Sting (GSD)
Comments: I should really watch 8th Team again to observe Norris, but he did take on Gundam types in a mere Gouf. Rarabal Ral did the same against the classic Gundam, so there you go. Next we have Yzak--yes, Yzak. Seed's "druggie trio" were a formidable threat together that even gave Kira trouble, but when push came to shove Yzak was able to defeat two of them in an admirable effort. Seabrook had a great Gundam, but he and Cecily also took on Iron Mask in a very formidable mobile armor. Well done, I say. With sufficient hardware, Athrun could challenge anyone in Seed. Next we have Duo, who once barely fended off Wing Zero and took on Mercerius and Vayeate at once. He was also good at using Deathscythe's strengths.
After that, I think everyone toward the bottom of the middle tier is roughly comparable. I put Tieria above Rey since Tieria actually defeated opponents outright (zing!), and Tieria was basically piloting a battleship of a Gundam all series long. The rest are all very talented and can make a respectable showing anytime, I just don't think they are particularly distinguished. I put Quatre above a few others by virtue of his brilliant mind.
Yeah, GSD's trio didn't impress me. They were being chased by one Gundam and two Zakus, and they couldn't walk all over them. Stellar died despite piloting a doomsday weapon. Aeul and Sting did nothing impressive. Yawn.
Low Tier
Shiro Armada (8th Team)
Lunamaria (GSD)
Christina (0080)
The 8th MS Team (sans Shiro)
Comments: Not much to say here; these are basically the foot soldiers that had the advantage of excellent hardware. Unfortunately, circumstances don't allow them to develop their skills or really show off.