X is my favorite character of all time, and has been ever since I finished the first Mega Man X game as a kid. So, for me it's X by a country mile.
I do love Zero too, don't get me wrong, and he and X make up the most badass, powerful duo in all of gaming. But when it comes to one or the other, it's X every time. His very name is a variable that represents his infinite potential, potential that is realized through his unique capacity to suffer and feel empathy for others, which is not something Zero (or any other Reploid, that we know of) is capable of, at least not in the same way.
I also love his growth throughout the series. He starts off in X1 as a rookie with Zero as his mentor, and by the end of X1 he's grown so tremendously that he's equal to Zero in power and remains so throughout the series. Much later on, in one of X6's endings, Zero himself admits that X has surpassed him. In X7 he falters as his ideals push him to leave the battlefield, but he comes back more powerful than ever once you unlock him and is enormously powerful in X8. Finally, in a really cool example of things coming full circle, X steps into the mentor role for the Zero series, guiding his best friend as Zero once guided him.
Both of them are tremendously powerful, no doubt, and neither one would ever win in a complete blowout, but at the end of the day, as powerful as Zero is there are hard limits to that power; and not only that, Zero is shown repeatedly to be rather fragile, dying or being taken out of commission several times throughout the series. X's potential strength, on the other hand, is limitless, and we see that brought to bear in his various armors throughout the series, which extend his capabilities beyond anything Zero is capable of (mostly). X's weakness is that he holds himself back because of his deep aversion to war and violence, but his unique capacity to care, suffer, and feel empathy for others means that when the chips are down and the occasion calls for it, none can compare to X.
I fucking
love X. He's just impossibly badass, and he's also a lot cooler-looking than Zero, whether it's his default form or his incredibly slick Command Mission design.