Zero and Megaman Zero? What is the difference?
Solution 1:
There is only one Zero. The Zero featured in the Megaman X and Megaman Zero series are the same, although Zero is 100 years older in the Megaman Zero series. The Marvel Vs Capcom 3 cut scenes are non-canon, and play no role in the storylines of the respective franchises.
The Mega Man wiki contains the full history of the character if you are interested.