You know, I've been wondering this for a long time but doesn't the megaman franchise have a set order of events?
X series goes into Zero series, Zero series goes into ZX series then Legends happens Battle Network series goes into Starforce series
Classic series has no actual ties to either series the running theory for decades was that Wily created Zero who proceeded to slaughter the entire classic cast before being sealed away and Light built X in that period was proven wrong years ago,too
But if ZX leads to Legends then which route for both games is canon, the little ads from back in the day implied the two protagonists from both games would be working hand and hand with each other but in the game proper they never once interact and some people theorized that the other character you don't pick dies but so far there's no proof of that and finally both routes in both games end on massive cliffhangers.
Oh well, it's pointless to mull over, I'm just rambling for the sake of it because it's been bothering me for the past 30 minutes. Capcom's never gonna fix the plotholes and cliffhangers of the X to Legends chronology especially since that Mega Man 11 game didn't do so well, the next X series game is a crappy mobile title and unless they can be convinced a megaman game could do sells numbers on par with Zelda or Mario mainline titles why are content to just release collection packs like these over and over and over and over again.
It's just loose connections for the most part, really. It's confirmed that each series takes place in the future of the previous one, but the actual way things connect has been mostly ambiguous. It's a bit frustrating but at least it provides healthy fan speculation. And it allows Capcom to keep making games in these series. (Except for Zero, that one definitively ended.)
I do know that Mega Man Zero 1 begins with Zero being found in "stasis" barely hanging onto a run-down, decrepit stasis pod that he ended up falling out of. This is a direct reference to Zero's ending in X6, where he decided to be put into stasis for some reason. Thanks to X7 and X8 happening, it's assumed to be farther in the future than just "shortly after X6's events." Hell, the X series was supposed to end with X5 but Capcom execs got greedy and messed up the story.
As for the Zero series...I have NO idea what's with Omega in Zero 3 and why its real form was actually Zero's real body, making the one you're playing as a fake replica with...Zero's data transferred to it. Nothing about that twist makes sense in relation to the X series. And the ZX series was supposed to be a trilogy I'm guessing, but sales dictated that it would be fruitless to continue. A shame since there was a direct cliffhanger at the end of Advent if you finished it on Hard. ---