With a founding of 100 years ago, Zero could be present to end the war. However, the story is clear; X is a lone hero that ended the war and fought for 100 years without Zero. Despite this, X and Zero saved the world together, 100 years ago? How can X fight for 100 years when there is no war after Neo Arcadia's founding? How can X be a lone hero when Zero wasn't sealed yet? How can X and Zero save the world together when X is a lone hero that ended the war, and fought a century without Zero?
The way I see it, the confusion of the statements and dates is due to Neo Arcadia's coverups of history. Zero, who's the very source of Irregularity, fought together with what Neo Arcadia conceives as the shining light of hope, X. That doesn't really sound all that great now, does it? Likewise, they deleted Vile's involvement with Neo Arcadia from the history tracks in order to conceal the fact that the government was partially backing up Vile's doings up to the point when he revealed his true colors and wanted to eradicate everybody on the planet he did not deem worthy in order to fulfill his twisted ideology.
To me, it's like this:
X fought alone during most of the Elf War (since Zero had been sealed away and was being studied by what was to become Neo Arcadia) and therefore most of the history records say that it was him who was the defining factor that contributed to the end of the fighting; that he was the one who brought down Vile. Zero appeared pretty much just during the final stages of the Elf War in a copy body, backing up X whilst the Big4 (if they were already around at this point) were busy with crowd control as Repliroids all over the planet tore each other to shreds (by the time of Z1, they had heard of Zero, but never met him face to face. They also seem to be familiar with Omega, as they knew who they were dealing with onboard the crashed Forbidden Ark, but did not seem to have encountered him before either. Same with Vile, they [Harpuia] only knew his name and what he had been infamous for).
Zero turned the tide of the battle by "bossing around" the Darkelf to have her direct all Irregular forces on Vile himself, therefore forcing him to send out his trump card prematurely and without his near all powerful abilities he would have gotten with the Darkelf. X and Zero defeat Omega. However, Zero decides that him being around is too dangerous for the world as history has proven several times over that the bad guys are really interested in the destructive and corruptive potential he possesses and goes off to sleep again, this time with the intention of leaving the world in X' hands, period.
For the next century, X and the Big4 deal with the problems of the post-Elf War world, building Neo Arcadia, trying to rejuvanate the planet and dealing with Irregular criminality, up to the point where X comes to the conclusion that fighting doesn't mean anything to him anymore because no matter how hard he struggles, history will eventually repeat all over. He vanishes to contain the Darkelf with his body's power and somehow his soul transcents into becoming a data lifeform.