Which could easily be a criminal act, by your own argument making him Maverick.
What I'm trying to say is, originally Irregulars were Repliroids and Mechaniroids who acted completely insane. VAVA was technically not completely nuts yet. He completely was doing incomprehensible stuff. He enjoyed blowing crap up. And he was part of the 17th Unit, Sigma's unit. Wouldn't be too good for the reputation of the Ace Hunters if one of them turned Irregular, now would it? So finding out what's wrong with him would become a priority, in case his behavior might have been caused by a virus that could easily affect other Hunters. Better to research it than to terminate a possible cure to a possible infection.
As time went on, Repliroids who did criminal things while being unaffected by the Irregular / Sigma Virus showed up. Arms dealing, robberies, whatever floats your boat. During that time perioid, the Irregular term was being expanded. That's at least how I see it. We all agree that it was originally just a definition of Repliroids running riot, but as time went by, Repliroids, having free will and all, could do evil things completely on their own, starting the whole dilemma with X' circuitry and what not. I honestly don't see why Lumine's "revelation" was so ground-breaking.
By my own personal definition of Irregular, I would already categorize Marino as one, but that does not mean I would demand that X shot her on the spot. What I'm trying to get across is, I believe that there would have been quite a few people in the Hunters, in the government and in the general public who would have demanded that he would. Surely theft is less dramatic than threatening to annihilate mankind, but it's still a crime and major offense and people are getting more and more paranoid as the Irregular Wars drag on, with the humans being completely utterly dependend on Repliroids fighting other Repliroids to save their skins.
In Command Mission X does seem more all-business, but then it is a good deal in the future. He doesn't hesitate as much as usual. Still, I didn't see him as lacking compassion. He does question Scarface and Epsilon as to their motives, trying to understand what's going on in their heads.
I might just be the stoicness of the cutscenes because there was so little movement (or facial expressions for that matter) in them, but X always seemed to me like he was getting tired of reasoning with his enemies. Sure, he questions Epsilon and his buddies as to why they rebel and all, but still, I never got the impression that X was trying to think of a third way to end the conflict other than blowing up his opponents or expecting them to miraculously surrender and hold hands. "You don't want to talk? Fine, let's have it your way."
I've been getting the impression that by the time of Command Mission, X somewhat subdued his sub-conciousness due to the onwaging Irregular Wars and tried to believe in society and the system behind it; the hierachy of the Hunter command structure. His superior told him Liberion/the Rebellion was a threat to all mankind, so he carried out his orders and put a stop to them.
And besides, and again, just by my own impression, I never had the feeling that X, even when he questioned Epsilon, Scarface and the others of the Cadre, would have not killed them or at least taken them into custody.
Exactly. My point is, how is Sigma less evil than Copy X?
Have I ever questioned Copy X' alignment? The thing with Copy-X is that he believes he is automatically right because he's the perfect copy of the legendary hero Rockman X who saved mankind a century ago. He's got that massive reputation behind him which boosts his ego to unknown ends of foolishness.
How is X supposed to let that slide?
Thing is, the real X didn't bother to confront his copy until Z3. During the events of Z1 and before, with his body still intact and thus a remaining link to the physical world and resting place which wouldn't cause him to wither away into Cyberspace, he could have easily done something. Try to reason his copy, or the Shitennou for that matter. But no, he chose to remain asleep and handed the job over to Zero while the house was burning down.
Marino is a criminal, a thief, but she is not an Irregular. That alone shoots down that notion.
She is wanted for the crimes she's committed. The thing is, Gigantis was being threatened by Epsilon, so X overlooked her rather minor criminal background and took her into the party. We don't know what happened to her after Command Mission, she might have just vanished in order to escape custody and X chose to overlook it since she helped him.