Yes, however none of that necessarily implies his story to be inconsequential.

Different game mechanics do not equate to non canon. And though the game may start out with only as much plot as Megaman 2 did, the multiple endings are much more elaborate than nearly anything else we had in the classic series.

Firstly, this was the first time Protoman and Bass took a really active role in opposing Wily. That, in and of its own, is a significant plot development, especially since Bass was made by Wily. Secondly, you did not mention several important things. Megaman's ending in Power Battles shows us the moment Light realizes he needs to create a robot capable of making its own decisions. Protoman's Ending in Power Fighters reveals he has a fatal flaw that will eventually kill him. And of course, the fact that Duo can sense evil energy from deep space, which we cannot discount as non-canon just because his presence in the game could only be a way to promote MM8 (don't get me wrong, it totally was meant to do that, but as said before it doesn't necessarily have to be only for that and make his story rubbish by default)
Finally, considering that, as you point out, X4 had already revealed a connection between Zero and Wily as well as the Maverick Virus, believing that Wily's other project brought up in the same speech ha makes about Zero is anything but the virus seems excessive caution to me.
All the more so when in Power Battles Wily only decides (like Light decides to make a self determined robot) to make a stronger robot to defeat both Megaman and Bass, whereas in this one, the game with space robot Duo coming back to hunt for Evil Energy, he now has blueprints and also brings up this other project

And that makes it somehow non-canon? Because it was aimed at the only people that actually care about canon in the first place?

Ok, I'm sorry to say but you clearly don't know enough of the subject matter here. It's not that you are obliged to of course, but you can't shoot down my parallel there without that knowledge.
The Zelda series works like this: every one or two games Nintendo makes a new Link that lives in the same world but in a different age than the previous ones. Early games in the series had very loose connections and this is why there's all that timeline theorizing going on. The 3D games, on the other hand, have clear and definite ties to one another. Majora's Mask, Twilight Princess and The Wind Waker all are tied back to the events of Ocarina of Time, whereas Phantom Hourglass and Spirit Tracks tie in with those of The Wind Waker.
All these connections are set in stone, even though the only games out of those that feature the same Link are respectively Ocarina of Time-Majora's Mask and The Wind Waker-Phantom Hourlgass. Similarly Adventure of Link continues the story of the first Link we've known from where the original Legend of Zelda on NES had left it.
So yeah, Zelda canon is a reality and Nintendo has confirmed several times that they have some big complex document to keep track of it. They apparently prefer to keep it for themselves because they realize a lot of fans continue to be interested in the games also (if not mostly) because they can nerd out over whether Ocarina of Time is still the "Seal War" of A Link to the Past's backstory or not.

I dunno Duke Serkol, you're pushing all this stuff so much that it sounds to me like every Megaman related thing put out by Capcom HAS to be canon no matter what, in your mindset. Like there's just no possible way that it couldn't be in the slightest despite any possible argument.

I suppose you'd like to inform us all about the great significance of Megaman Soccer and Megaman Battle and Chase as well?

Sometimes companies do make something as a spin off or just for fan service with no original intent of having it canon. Perhaps after the fact they come up with ways to link it together be it for fun or just trying to please people like you amongst the fan base, but it's very possible that somebody at Capcom just said one day, "Hey! Wouldn't Rockman fans just love a Rockman fighting game? Let's make one. Throw in lots of characters! Let's make Protoman Bass etc. playable. It'll make us a lot of money!" and they may have come up with an interesting story for it but was it really intended to be connected? It seems like it was all connected as an afterthought to me.

I dunno, that's just my opinion. As for what I personally believe, as much as I enjoyed the stories of some of the games, particularly some of the X games It's just such a mess between bringing this guy back for this reason and whatever else may happen that doesn't seem to make any sense I just don't really care anymore. I like mega man games cause they are fun to play, have great music and cool looking characters. I'm not too worried about where this complex, plot hole patched, story is going, as long as it still delivers on the other fronts.

Don't get me wrong I'm not trying to dismiss your opinion or anything here. You've provided a great argument but I don't think continuing this discussion is really gonna do much else for us...

If I'm wrong then whatevs. Feel free to continue but I've been watching you guys go back and forth for awhile now and it just seems like you've hit a dead end. Neither of you seem like you're gonna budge.