I was wondering how he came back after X3....
Maybe canon-logically speaking he never did die in X3. After all, didn't you have to trigger his death by playing as him right at that moment?
X5's endingalso would not be too well off with Zero 1's intro. If Zero actually Dies in the X series, then why is he simply deactivated in Z1?
he was nearly blown to bits, reduced to his usual torso and an arm, Zero1 has him lying in an abandoned lab with the only visibly missing limbs being his forearms. X6's Zero sealing actually goes a lot better with the Zero series than X5 did. all X5 works for, is the explanation of X keeping Zero's saber.
Zero has a habit of being blown up to near bits and restoring himself, and he does look pretty beat-up in the beginning of Zero 1. Plus, it isn't his real body, so at some point, someone could have taken his corpse, given him a new body, but took his real body and fixed it up for Omega. It's possible that Wiel did it at some point. Why give him a new one? Who knows, maybe Zero 'grew' himself a new body.
X6's ending doesn't fit well with the beginning of Zero 1 either; Zero went to sleep after the Elf Wars, so how could he have been sleeping if he was helping X fight in that battle?
If anything, what they need to do in X9 is: kill of Axl; he had no part to play in the Elf Wars, so he has to be gone by then, be it by death or simple resignation. They also need to have the start of the Elf Wars thrown in there. I don't care if the battle just starts when the game ends, but it HAS to be thrown in there somewhere. That way, there's a perfect tie-in into the Zero series, and less questions can be raised.
They also need to come up with a game between Zero 4 and ZX; how did Ciel get ahold of Zero's data to make the Biometal? Just how the heck did Zero lose his body but gain a new one? Even if they just released a manga stating all this I'd be happy.
The plot and initial setting of Z1 was vastly different from the actual game, which had been heavily modified to work with the Zero Ending of X6 (Z1 was already in production when Capcom decided to make X6, but came out after X6. X6 was November 2001, Z1 April 2002). Originally, Ciel was supposed to be something like a Cyber Necromancer who would use Cyberelves to bring back Zero from the grave. But since X6 established Zero as still alive, only to seal himself again in the end, the way Zero was put into this story was altered to make sense with his X6 ending. Too bad X7 ruined it all.
I never did get why they completely trashed Zero's ending in X6, but I remember someone saying something about how that they MAY not be canon, and the events may have happened farther into the future (though, I doubt it was too far, isn't the Zero series about 200 years after the X series?)