"A hero is more than a person, a hero is a belief. A belief that, against impossible odds, the world can be saved—and that the world is still worth saving. Heroes inspire that belief in us. They renew our faith and give us that most precious of all gifts—hope. The world needs heroes. That's why, when a true hero arrives, the world will honor him." --Thus states Xbox.com's Halo 3 site as part of the "Believe" promotional campaign. It references a scene in Halo 2 in which Avery Johnson tells John-117 to put on a show for the cameras at the awards ceremony, "Folks need heroes, Chief, to give 'em hope."
John-117 is the "hero" of the Halo series, a super soldier wrapped in robotic armor. He is the last of his kind, as the Halo: Combat Evolved manual describes, the awe of every soldier around him. This is the character of which the player takes as their persona, an unstoppable force of humanity serving only the UNSC, his orders his only guide. His minimal personality is only visible through his interactions with others, specifically Cortana and Captain Keyes.
The books show us the backstory. He was originally a civilian boy of six when he was selected among 74 others for the secret program SPARTAN-II, and forcibly inducted (read: abducted) into it. His family was not informed of this, a flash clone created and left behind in John's place. The clone would have no knowledge or experience of human existence and would eventually be a victim of metabolic cascade failure, an incurable series of neurological diseases leading up to death.
Dr. Halsey had meticulously constructed the training environment for the Spartan-IIs, based on the training of the original warriors of Sparta, after which the SPARTAN projects were named. The training would be extremely strenuous for their age, comparable to that of Marine training, with the noted exception that she was not working with volunteers. The Spartans would wake at an early hour to be led to their "morning calisthenics", a series of 100 jumping jacks, sit-ups, squats, knee bends, and leg lifts, before given salty water and a run around the compound. Any Spartan who resisted would be struck with an electric baton, as John was before he learned to follow orders. They were then led to their class on strategy, and their first meal of the day: stale crackers and milk. After the class, they were taken to an obstacle course where the last team to complete the task of ringing a bell would go without dinner, a most bountiful meal compared to breakfast. What followed was John completing the task first, but leaving his team behind and causing them to lose dinner as a team. John learned to function for the good of the team, as opposed to just himself, and they won the next day.
What necessitated such a violation of human rights was the growing rebel threat. For decades, certain groups in the outer colonies had desired that their governments be split off from the UNSC, a belief that led them to violence and terrorism. This threat had led Dr. Halsey to conceive of a revamped version of the earlier SPARTAN project (later referred to as the SPARTAN-I program), using superior augmentations at the onset of puberty as opposed to those given to the full-grown Marines of the SPARTAN-I program. That the SPARTAN-II program required the abduction of children was an unfortunate necessity for the good of the UNSC in Halsey's mind.
This is not intended to be a criticism of UNSC policies, although I don't see it as ethical in the least. This is intended to show that although John has done extraordinary things, it is not his own doing. John was just reacting to forces beyond his control, eventually transforming into a brainwashed tool of the UNSC. As Cortana puts it: "The Spartans live a pared-down, difficult and often cruel existence. Their loyalty is bred into them, not chosen. (...) The original Spartans had the advantage of a former civilian existence. Spartan IIs are equipment. And for better or worse, they're effectively brainwashed."
Compare this with Avery Johnson. He spent his childhood as a typical civilian, living with his aunt as the result of a custody dispute when he was six years old. Much like John, he later couldn't remember much at all about his previous life. However, his new life with his aunt was much more pleasant than that which the SPARTAN-IIs would face many years later.
Avery knew of the rebel threat. Though he believed in their cause, he also believed that the manner in which they tried to bring it about was immoral. So, despite his Christian teachings, he chose to join the UNSC Marines. This is a notable contrast with John, who simply leaped into battle in faith that his superiors were undoubtedly correct in that the rebels needed to be taken out.
Avery climbed through the ranks, and was selected by the ORION project for participation in the SPARTAN(-I) program. The final choice, however, was his. He was recruited into the SPARTAN program, where he received augmentations to make him the best soldier he could be.
After the SPARTAN program was disbanded, many of the Spartan-Is retired to start families. Avery, however, continued to fight in the war against the insurgents. He collected his share of psychological issues, but pushed them aside to do what he felt needed to be done. He continued to fight well into the Covenant war, retaining his fears, hopes, doubts, passions, and humor - what makes him human.
A hero, in my mind, is about someone who overcomes great obstacles to do what must be done. This can be applied to both Avery Johnson and John-117 to a reasonable degree. However, Avery could have turned back at various points in his life - an option John never had. Obstacles aren't just about hostiles in your path; they can be doubts and temptations.
John had the SPARTAN-II training, the armor, and the power. But he never actually chose to fight - it just happened to him. Avery may not have as much strength as his Spartan successor, but he ultimately fought harder. Therefore, I would have to say that out of the two of them, Avery Johnson is the hero of the story.
"They ennobled all of us, and they shall not be forgotten."