That's the reason why Netto acted like he did in the manga.

I'd personally that the EXE manga was a wee closer to the games, but then, it was no continuation until the sub-plot "Bug Monster" came along. =/
I'd like to see a MM story outside the games that's accurate, but also enjoyable, wich is the problem. The Jap manga (Mega Mix is what I'm referring to here) never made it to the US, but I'd belive that a huge part of it had a chance to continue. Contrare to belive, I'd love to see a US MM comic. Archie.. I don't know. I just don't down-right trust the comic because I'd be sckeptical about the heavily influince about "Archie and Friends" that would pop up in the story, confusing the readers. *Insert Burger-shaped RM for the spirit of the Burger Miester here*
Marvel I don't trust either. I'd worry too much, but heavy cameos from the Marvel universe would kill the comic, or the comic would stray too far off the plot. (Likewise, X or Mega Man in a relationship while slowly Dr Wily/Sigma is an inch closer to dominate the world)
Wich is why it'd be a better option to leave the comic business to Lengends, it's comical, cute, and, serious. just right for all audiences. (Seeing how it's perfect enough for a Manga/Comic spinoff would have business booming, enough for a Lengends 3)