My problem with most of this that there is no real judgment calling on either of their parts. It always ends the same way: with a fight and the suspected Maverick dying. It's the traditional trapping of the Mega Man action game. But with the X series, I think the games' could've handled both the gameplay and this dubious case of who-or-what-is-a-Maverick more intelligently by giving players some more choices and more consequences.
It wasn't until recently that Capcom gave Westerners manuals or guides outside of Japan on what they actually do with the Mavericks. I know we are not expecting a Bioware type game where your actions effect your morality meter but I agree that gameplay did need to accomodate this. In almost every X game, it always this:
Eight Mavericks, Irregulars or whatever are attacking and X and Zero must stop them
(X and Zero beat the level and get to the boss, busts down the door)
X/Zero: What is going on here?
Boss: I am evil and just want to do evil things, lol!!!
X: Is there any way we can about this?
Zero: Why aren't we fighting yet?
Boss: I don't want to talk, I want to destroy things and I want to beat people up for no good reason!
Zero: Have it your way!
X: We could avoided this!
(X and Zero beat boss)
Alia: You got the bosses weapon. It turns this guy wasn't evil at all but Sigma or some other Reploid manipulated this guy into commited these atrocities, he was actually nice guy until he went crazy some contrived reason. A pity though...oh well, on the next Maverick.
*rinse and repeat*
It would nice to put in some sort of morality where there was no clear hero or villain and even X admits that he may be the bad guy this time. Capcom will not allow this to happen to their blue bomber but it would be interesting what would happen if the line between Irregulars/Mavericks blurred.