Megaman X as A Totally Different Robot from the Original Megaman
Well I've been in the wrong and here's Capcom's official word that confirms Megaman X is NOT the original Megaman. So we don't know what happened to the original Megaman, maybe he just simply burned off and why he wasn't referenced in the X series is something.
From Club Capcom (read here):
How is this connected to Rockman?
The new “Rockman X” is, to put it simply, a game that is set in the same world as the “Rockman” that appears on the Famicom. Only, the “Rockman” time period is set in 20XX A.D., while “Rockman X” takes place in 21XX. That is, “X” is set in a slightly later era.
Our protagonist this time is X, who is of course an entirely different person from Rockman. He’ll still have the Rockbuster on his left hand, the helmet, and everything that’s come to be associated with Rockman, but he is in fact a separate character. He is merely inheriting the world stage of the “Rockman” series, and that means the same familiar types of enemy characters will be around as well. Please think of this as new series set further along in the same universe.
Based on Club Capcom, Megaman X is not the original Megaman. Rather he's an advanced version of Megaman. That means Zero can't be Bass either. Just me thinking since Megaman X is a new generation robot called a "Reploid", some events in the original Megaman suggest that Dr. Light's AI was already working. For example, Megaman wanted to kill Dr. Wily and nearly broke the Asimov's Law of Robotics. X's advanced system compared to the original Megaman was more advanced, which Dr. Light saw as a threat if it wasn't tested properly... remember Megaman hesitated to shoot Wily but X may break that law. The rise of human-like A.I. was already evident with Protoman's willful defection from Dr. Wily to Bass' turn from villain to anti-hero.
So why did Dr. Wily create Megaman X? One may theorize that Megaman X was created because the original Megaman may not last long anymore. Also, maybe Zero was awakened and they barely made it. No reason was given, maybe he felt they needed a hero in the future so Megaman X was created in response to that need. Nothing was known to how Dr. Wily was finally defeated. The answer may lie in Zero's creation as Dr. Wily's attempt to get rid of both Megaman for their years of rivalry and for Bass for not willing to obey him.
However the statement "separate character" may not always suggest that Megaman X isn't the original Megaman. Supposedly Dr. Light found Megaman severely damaged and started to do repairs. So in the process, Classic Megaman lost all his memories to the point he becomes a separate character. You can think of Ginrai becoming Victory Leo. Victory Leo is a separate character who was previously God Ginrai. Being an "entirely different person" was also this. Remember Vision in Marvel Comics was created from the original Torch android. So Torch and Vision are more or less the same entity but separate characters.
So why did Dr. Wily create Zero? Remember he wanted a robot to destroy both Megaman and his rebellious creation Bass. It's unknown if Zero ever faced both Megaman and Bass. All that was known was that Zero was sealed off by his creator. Megaman X was sealed away for the reason of testing, perhaps Zero also had the same reason. Dr. Wily may not be able to use Zero at the present but certainly, the latter can emerge later to destroy Megaman X. Zero was most likely a legacy character and Dr. Wily's successor. He knows he won't live long either.
For Zero, what's interesting is that he's Dr. Wily's best robot. Remember when Dr. Wily created Bass, he discovered Bassnium. Dr. Wily also gathered the Evil Energy from space which may have led to Roboenza, and later the dawn of the Maverick Virus. Zero was the carrier of that virus. Perhaps Dr. Wily created Zero from the same blueprints that Bass was based on. In short, Zero's programming was meant to be more advanced than Bass. Remember Bass rebels against Wily and I guess that characteristic went into Zero as well. However Wily may have decided to seal Zero to someday continue his work.
I guess Dr. Light finally knew of Zero's existence and decided to create Megaman X in response to Dr. Wily's latest threat. Although Zero was sealed off, I guess Dr. Light figured out one day that the former will be awakened. Dr. Light created Megaman X to be tested for 30 years which instead reached 100 years.
On the other hand, only if Capcom will explain how the original Megaman era ended. Sad to say but Inafune is no longer in Capcom.