>>6106114At the time, X5 was to be the end of the X series, so Zero going to sleep at the end of X5 and waking up in Z1 made sense. Neither X6-8 nor Z2+ had been considered during Z1's production (IntiCreates was thinking it was going to be a single spin-off game), so they just did the +100 years thing that X did to the MM series.
When X6 came out and IntiCreates was asked to make a sequel to Z1 is where the timelines fall apart. So now the timing of X5's Zero ending is in flux, and the Elf Wars happens sometime after X8 (or X6 or Command Mission, whatever). Plus we don't know exactly when Zero got put in his MMZ body.
It would have been best if Omega had the X-era Zero body, but they couldn't do that (Z3 was already scrapping the limits of what they could do).
Hell, IntiCreates thought Z3 was going to be the last game, then CapCom said "You're doing a Z4, right?" So even the tighter plot of the Zero games gets wonky.