Now why I thought Megaman X and Megaman are the same person. In Megaman X5, try to look at Sigma's dialogue in the final fight scene. Sigma declares that he acquired a "new partner" and that "they know each other very well" and "made a few robots" and "used to be a comrade of yours". Dr. Wily used to be a comrade of Dr. Light though how Sigma knew about these events that happened a century and some years ago. So it seems this makes X as an upgraded Megaman but rebooted of his memories. Though Dr. Wily would have died due to old age, it was possible that Dr. Wily managed to implant his memories into a reploid body, thus continuing his work in case everything fails.
So far, that wasn't released at all. So when we think about it in Megaman 7, Megaman has started to display his own free will at a higher level but also his want to end the war. Both Megaman and Megaman X are seen to be pacifists. In Megaman X2, Serges could be Dr. Wily or a robot with Dr. Wily's memories. Either way, Serges displays some hatred for Megaman and in X6, Isoc seems to be another robot with Dr. Wily's memories or could be Dr. Wily.
Now for where they are different. In Megaman X, it was shown that Dr. Light created Megaman X as a new advanced system. So what is possible is that if they are different persons, the original Megaman soon became obsolete in the 100 years time (since X is 100 years after the original Megaman and heroes do die eventually) but both are pacifists at heart. So pretty much, if they were different persons then again Dr. Light could have deleted Megaman's memories and rehashed him into a completely different person which is my theory.