I post preciously few things not backed up with fact. And with facts I mean exact quotes from game, manual or other materials. As it is, without specific examples the burden of proof is still on your end. With bringing up just Isoc and Wily as your best case, you're not showing well how much you actually pay attention to plot.
See, and this is where the problem is.
You say facts, exact quotes from games, manuals or other materials. I have no problem with those. It's your constant "GEE I GUESS IT'S OBVIOUS THAT THE CREATORS CLEARLY MEANT MUCH DEEPER STUFF AND THEY TOTALLY DIDN'T JUST RUSH THE PLOT OF MEGAMAN X[insertnumberhere] JUST SO THEY CAN HAVE A REASON TO KEEP SPAMMING MORE GAMES!" attitude that I have a wee bit problem with.
Why? I'll tell you why.
Plot from Megaman X, which I'll use in this example, is laughably bad and simple. By looking so much into this, and trying to make connections of various stupid crap left unanswered, you just make yourself look kinda stupid. Of course, I'm not forcing you to NOT DO THIS, I'm just saying that in my eyes it looks delusional. Not a very bad and dangerous kind of delusional, but still.
Megaman Zero, for one, is a bit different, and I actually enjoyed all those different plot elements from it... the audio dramas and whatnot. Since it really seems like they actually put some thought into the plot, even if still a bit simple, it was much better. It didn't seem forced, it didn't seem stupid. It felt just right. This is a game, which is actually worth exploring with various theories... and yet I wouldn't dare look too much into it, when it's obvious that even in this case, the creators obviously... didn't think that much about this or that.
So, to summarize what I'm trying to say here:
NO ZAN! I'M NOT TALKING ABOUT YOUR ACTUAL EFFIN FACT BACKED UP THEORIES WHICH DO MAKE SENSE, BUT ABOUT YOUR CONSTANT "LOOKING TOO MUCH INTO IT" WHICH MIGHT SEEM TO MAKE SENSE, BUT OVERALL ALL OF IT FALLS DOWN WHEN YOU REALIZE THAT MEGAMAN GAMES HAVE, FOR THE MOST PART, [parasitic bomb] PLOT WITHOUT ANY WELL MADE CONCLUSION (except Zero, BN and Star Force, more or less. But I don't count these since they actually have decent plots which work)! SO BEFORE YOU TELL ME NEXT TIME ABOUT HOW MUCH DEEPER AND MEANINGFUL THE PLOT OF MEGAMAN X IS AND HOW FOOLISH I AM FOR NOT PROVIDING ANY "PROOF" FROM THE HUNDREDS OF YOUR POSTS WHICH CONTAINED THESE THEORIES AND WHERE MOST OF THEM HAVE BEEN WIPED OUT BY THE FORUM CRASHES PLEASE REMEMBER THIS:
[spoiler]"OH LOOK IT'S SIGMA AS THE BAD GUY AGAIN! I DIDN'T EXPECT THAT AT ALL! WHOOO!"[/spoiler]