It's good that you brought up Maverick Hunter X, since there are some issues with that game as well. Are we to assume that it retcons [or was intended to retcon] the original MMX? For instance, it heavily implies that Cain is killed in the missile strike Sigma made against the city. Yet Cain is clearly still active in X3 (and briefly mentioned in Japanese X4 i think, not 100% sure). Had they continued with this Maverick Hunter "reboot," I doubt Cain would've been involved in any way, much less a "background character" or anything.
The flashovers are much larger than the actual craters left by the missiles. It is entirely possible that it was meant to be a cliffhanger. Yknow, to be edgy. Besides, Wily has survived worse.
Besides the Cain matter though, There are no contradictions or retcons really. Anything that wasnt in X1 is just new material.
Only part that was changed, and its something that bugs me, is X being able to defeat Vile in the intro stage. But he loses anyway, so its not too big a deal.
On Cain's X4 mention- The memo from Cain Labs was made by Capcom of America. It is not canon.
There's no reason for him to delete his mind, as like you say, it's not in his character. He's been sleeping for a century, hibernation sickness gets the best of him, he forgets his life as Rockman (just like Zero when he awakes in MMZ, doesn't remember a damn thing from his Maverick Hunter days, throughout the series).
Again, refer to X's conversations with Light during his construction. Light calls him X, and X asks if that is his name. To which Light says it is, and explains it's meaning. he also does not know who Light is upon his initial activation. To which Light explains that he is Dr. Light, and he created him.
All throughout the flashback, and whenever Light refers to X it is as a different Robot.
Even in the Warning in the original Mega Man X.
"X" IS THE FIRST OF A NEW GENERATION OF ROBOTS WHICH CONTAIN AN INNOVATE NEW FEATURE - THE ABILITY TO THINK, FEEL, AND MAKE THEIR OWN DECISIONS. I guess we're picking & choosing what to follow, since there are contradictions in the story with Cain's death, when exactly Sigma's true motives kicked in, etc.
Cain's death is the only real point of debate. And for understandable reasons. Sigma's plans definitely were already in effect by the beginning of Day of Sigma. After all, he was the one making the construction Mechaniloids go berserk. Some time before Day of Sigma is when he decided he would rebel.
Sigma tells him that the "old man" he's in league with has passionate hatred for X, and knows him very well. This implies that either X/Rock are the same & Wily was always aware of this, or Wily just simply THINKS that X is his original nemesis, unaware that they are separate entities.
Wily became well aware of X some time after he had Built Zero and sealed him away due to his cognitive flaw causing disobedience and extreme violence. Zero's original purpose was to defeat both Bass and Rock, and help Wily take over the world. But when Zero turned out to be defective and was sealed away, That plan was put on hold. At some point though, either during or after X's creation, Wily became aware of him, and Zero's purpose was changed, and his mission became to destroy X, and therefore settle Wily's rivalry with Light. Zero would fight and kill X.
Unfortunately, circumstance changed all that, and fate had it that Zero was himself infected by the virus leaking from his capsule, which caused that W on his head. You know the story from there. He became good, Sigma became evil.
Wily however, as stated by Inafune, died in the interim, and was "brought back by the virus". Serges and Isoc are certainly Wily, and they both prove it. And Wily's goal is to get Zero to kill X. or just to kill X in general.
Is it up to the player to decide, once again? It's a shame that these sourcebooks & obscure Japanese interviews are easily overlooked by the casual MM fan, since they seemingly contain all the forbidden knowledge of our beloved characters and certain plot points (X's "Suffering Circuit," for instance. no one would have a clue wtf you're talking about if you were to bring up the idea of such a thing in the years before, you guessed it, a sourcebook revealed it!)
Good thing Udon has gotten all up in the business of Translating Mega man stuff. Who knows, someday we may get those.
At the end of the day, it doesn't really matter if he is or he isn't. The "spirit" of MegaMan remained present, even thousands of years later.
He is definitely the spiritual successor. "Mega Man" is not a name, it is a title. A title inherited by those who fight for peace.