It seems like quite a bit happened before the first game, and that the Maverick uprising was a problem long before Sigma turned and brought them under his wing.
Sigma was the commander of the hunters for some time, even after his fight with Zero.
X was also a hunter during this time, and it's implied that there are other capable hunters as well (such as Gamma, referenced by name as having fallen in a fight with Zero).
I think this would be way more interesting than any sequel, considering they likely won't ever touch the Elf Wars. You could swing it a number of ways, with X as the sole player character, a separate game/"campaign" for Zero after he turned good, or a new playable character, maybe even Sigma himself (who I Imagine would play very similar to Zero, as his original incarnation was a swordsman).
What do you think? Could it work? Would you be interested in it?