My favorite Gundam protagonists are the following:
-Domon Kasshu. Dude is basically the father of Kamina and Kallen. Hot blooded, irritable, thick as a brick, and badass like no other. Seeing him go from being an asocial jerk who couldn't talk to regular people let alone appreciate the girl who was with him, to a full blown master of combats fueled by the power of love, was definitely the best progression of any protagonist for me. It's hard to hate Domon.
-Judau Ashta. Judau is a goofy, laid back guy, who even after getting pulled into the hell that was the Neo Zeon war, never really loses his cheerful nature, even when he does get his act together. He was a breath of fresh air after the seriously messed up Amuro and Kamille. Judau also scares the bejeesus out of Haman Khan, which makes him pretty damn awesome. Also dude gets Roux in the end.
-Kamille Bidan. Kamille is the best part about Zeta Gundam. He starts out an unlikeable, horrible asshat, but as the show introduces other screw ups, Kamille pulls himself together and becomes a legitimately good guy. Also he pilots the Zeta, which makes you even cooler just by touching it.
-Tobia Arronax. Tobia is so awesome he prays to God to NOT help him so he can kick the asses of everyone on his own. Tobia is so awesome that he basically says Newtype theory is full of spit and that people are just adapting. Then he proves it. Tobia is so awesome that he is super awesome and deserves his own damn show.
-Heero Yuy. Heero isn't as cool as he used to seem, but I mean come on. Dude pilots the Wing and Wing Zero, is always doing crazy ass spy stuff, and cracks jokes in monotone. In fact, Heero's deadpan snark is probably what sets him apart from Trowa, whose character basically is not having any defining character. Also he threatens to kill Relena all the time, and he's the father of Sousuke Sagara and . . . Setsuna. But mostly Sousuke.
-Athrun Zala. He should've been the protagonist of both SEED and Destiny. Athrun is sarcastic, cynical, and has a better grasp on what is going on around him than everyone else. He gets all the honeys (except Murrue), and while the Infinite Justice isn't as awesome as the Strike Freedom, it's still pretty damn awesome. Athrun is one of the good SEED characters, and would've and should've been the protagonist.