I love this topic because it BEGS to be discussed. Every Gundam fan has their favorite. I came across this forum while just surfing the net while I was bored and I wondered what everyone's take was. Let me start off.
I personally think that Heero Yuy was THE BEST Gundam pilot. I give Amuro Ray credit because he was pretty badass himself, but he was a Newtype. Kira Yamito is another common candidate, but he was a coordinator. Newtypes, granted, are considered natural evolution so I think that it really can't be held AGAINST Amuro, but still it is an advantage. Coordinators on the other hand are artificial, so I think Kira is out of the running. Another two good candidates are Kamille Bidan, and Setsuna F. Seiei.
Let's talk comparative skills now, I'll build the case for Heero and then against the others. Heero has no natural advantage over other human, save training. We know that from a very young age he was tranined for his mission, we also know that this is why the Lightning Count, a lifer, could keep up with him. However, Heero was only 14. So he still has time to grow and hone his already impressive skills, the fact that in 14 years he can hold his ground against a man who has been piloting mobile suits since their inception is staggering.
Heero was also able to harness the ZERO system. This takes mental focus and willpower. He was able to repair his Wing Gundam in one night using parts from the Deathscythe, again, not an easy feat. Then the following day, he flys off into a battle with NO sleep. His prowess was not only in the piloting of a Gundam. He fought in a Leo against the Virgo Moblie Dolls and for quite a while held his own. Then, this time in a Space Leo, fought against the Altron and again held his own. Both suits were standard suits he stole.
Amuro Ray was without a doubt one of the best Gundam pilots ever, however, he was evolved. He also was the son of the designer of the Gundam. I fimly believe, although the anime never states this, that he had some knoweldge of the inner machinations of the Gundam prior to using it. That's why he was able to do what he did right out of the gate, again this is speculation. His early career was standard. He was an ace, but yet still the unevolved Char was able to best him time and again. Plus he was a hot head. He would break protocol time and again. Heero was a machine. Goal. Accomplish. Goal. Accomplish. No room for error, no room for mistakes.
Kamille was a girl, and I'll leave it at that. If you pick this guy....I'll be speechless...
Kira Yamito was the "Perfect Coordinator." He was as perfect as mankind could have made him. Although not his fault, this is an unfair advantage. Even with this bonus, and with his "seedbursts" I think that Kira in the Strike Freedom, fails again Heero Yuy in the Wing ZERO. While Kira was focused on not killing, Heero was focused on the bigger picture, stopping the whole war by any means necessary. Kill or be killed.
Setsuna F. Seiei is the only other contender in my mind to Heero. Natural birth but he evolved. But even before innovating, he showed skills. In the Exia he performed some pretty nice feats of amazment. I still think tho' since he was traumatized from his youth with the whole idea of war, that Heero who was able to have his demons but get the job done anyways was a better pilot.
There you have it, I've built my case and spelled it out for you. Let's have it out. Keep it respectful please and remember that we're just debating for the lulz.