It is not. Proto has that unstable nuclear core before Wily met him; in the original games, it was a solar reactor that was messing him up.
I think you got that in reverse. The mentioned "unstable nuclear core" is the one Wily gave to Blues. Light originally built him with the solar one.
Here's the excerpt from HeatMan and Delta's research into what the classic books say about Blues:
Upon Proto Man's completion, Dr. Light realized there was a flaw in Proto Man's power generator and wanted to repair it. Proto Man seemingly misunderstood Dr. Light's intentions, fleeing the lab believing the operation would destroy his individuality.
Proto Man remained isolated over time as the flaw in his power generator grew worse. But just before he would have ceased functioning, he was found by Dr. Wily. Dr. Wily replaced his solar energy power generator with an atomic power generator. He also modified Proto Man to have battle capabilities.----
Proto Man, serving Dr. Wily, attacked Mega Man on various occasions under the identity of Break Man. Due to the nature of his atomic power generator he could only battle for short periods of time.I don't remember there being any evidence that the two had met before.
Taking into account the above;
---ProtoMan: When you attack me, watch out for my unstable nuclear core... One big shock and we're both vapor, I'd say.---ProtoMan made clear cut mention of a piece of hardware he given by Wily. This is once again reflected in the following passage:
---ProtoMan: It's always been on my mind...what it means to be born with weapons in our hands. I haven't found the answer yet, but with the powers you've given me, I will crush your villainy.---And the narration clearly specifies ProtoMan's being born with weapons as after the creation of humanoid industrial robots:
---The year 20XX. With the advancement of science, humans were able to create industrial humanoid robots. Then suddenly, a robot with built-in weapons made for combat was also developed...---Which MegaMan agrees with, to his knowledge, there's no robot made for combat that precedes the creation of the Yellow Devil:
---MegaMan: This is a first! A robot made for combat?! Well, you're going to have to get out of my way!---Yet ProtoMan is the first humanoid robot ever created. This apparent contradiction is only explained by Wily having worked on ProtoMan's "rebirth".
That Wily is well aware of who ProtoMan is, is also reflected in the following:
---Wily: I have no need for a robot that won't take orders! Nuhahahahah...---"A robot that won't take orders", that is very much how ProtoMan described himself:
---ProtoMan: Robots are machines that follow orders. I'm a machine that doesn't, so what does that make me?---Wily wouldn't have said that line unless he was well aware of his origins. He says similar things to all the others, rejecting them for certain quirks in their design and personality.
So, Wily knows exactly who ProtoMan is. ProtoMan is equipped with a power core Wily gave him. ProtoMan is equipped with weapons Wily gave him. ProtoMan acknowledges all of this.
Finally, I believe I mentioned before that the Japanese sourcebooks postulated the possibility that the only reason why Wily could so easily reprogram Dr. Light's robots was because of the knowledge he had obtained from having worked on ProtoMan's systems at the time he changed his solar core to a nuclear core.
Given all of the above, how can it be that Wily and ProtoMan never met?
Light's rival could have become his assistant. There is no discontinuity. You're creating a fuss over it, but it's just not there.
You know, you're looking for an outright statement: Wily was not Dr. Light's assistant!
Why would such a statement exist?
Why would the writers go to great lengths to disprove a notion that's not part of their story to begin with? We all know the original manual for Rockman1 did not speak of Wily as Light's assistant. So it's only natural that any and all subsequent materials that are not subject to the exact same treatment as the MegaMan1 manual, will not address the matter at hand.
Why are you clinging to "Wily is Light's assistant" as part of some region specific canon when none of the later games acknowledge that fact? Literally all of the later games have chosen to keep the "Japanese canon" as its story. The very fact that they did not keep up with consistently adding: "Wily was Light's assistant" into their manuals state that they've discarded the notion.
Powered Up is simply the final nail in the coffin as it is a remake of "MegaMan1" that just as many of the other sources disregards the Wily assistant story of favor of Wily as the exiled rival.
If the story was "US canon" they would have once again changed their manual to reflect it; they didn't.
In that regard, your "US canon" is actually "EU/German canon" as I recall hearing from BTD/Saber that the German manual for Powered Up did re-include the notion.
And well, that's just plain silly. The assistant notion is just something made up by people in charge of localization. There is no region specific canon, it doesn't exist; there is only the story that the original writers themselves wrote before we went through the process of translation/localization.
The originals can be fan-mistranslated or differently interpreted, though (remember Mr. Shin mentioning "Yakasa"?). And, yeah, errors in localization are annoying, but apart from those in the X series, I don't think any of them have been large enough to care about.
I consider making up whole pieces of story about Wily as Light's assistant as a error big enough to be cared about. Likewise to MegaMan telling Wily to go die and that he's more than robot, likewise to ProtoMan telling MegaMan they both have the same creator.
Those changes give completely the wrong impression than the original story.
And yes, the X-series is even worse.