But Proto's line towards the end would imply that he knew Wily was a nutter before the events of MM1/MMPU (and that he ran off before he got the shades and scarf, since Wily doesn't recognize him). That's not the same past that leads up to RMRM or MM3.
He learned Wily was a nutter at the beginning of Rockman Blues (The title screen changes from Rockman Rockman to Rockman Blues, Rockman Roll, etc.) when he viewed that broadcast. As for Blues' shades and scarf, their origins are rather unexplained, it's mostly just a style thing.
Whether or not Wily recognizes him.. as we've discussed; I believe he does. Or at the least, if he didn't recognize him immediately, it's just because he had to look twice to comprehend it was really Blues standing there. But all of this would be conjecture. Really, as this single line is an anomaly, I think we'd better ask the question of what the original Japanese script said.
in the US game canon, it's "Megaman" and "Protoman" and not "Rockman" and "Blues".
So which is it? AquaMan or SpoutMan? YamatoMan or JapanMan? Treble or Gospel? Rock or Mega? Volnutt or Voulnutt?
In this case, everything has ben additive. Nothing has overwritten that point.
I presume all of this is true as well:
-The time institute Wily stole an experimental time machine from is called Chrono Institute.
-The experimental time machine Wily stole from the time institute is called Time Skimmer.
-MegaMan told Wily to die!
-MegaMan is more than a robot!
-Bradbury K. Wells, Times Staff Writer, reported on X's attack on the Maverick Production Facility.
-Serges was collecting Zero's parts.
-Serges was trying to achieve Zero's "unification" to fulfill a prophecy.
-Sigma should have studied the blueprints closer.
-Doppler used his Neuro Computer to prevent abnormal behavior in Reploids (even though said neuro computer is his own brain?)
-X defeated Vile years before the events of X3.
-Vile will haunt X till the day he dies.
-The galaxy is at peace after centuries of fighting the Reploid War (even though it's still 21XX, the war started several months ago and there is no peace?)
-Wily used to be X's comrade.