Zero era Zero isn't that much less haxed. He still has time manip, absolute zero, intangibility, attack reflection, some Regenerationn, life drain, and with the Tractor Shot can absorb attacks thrown at him to increase the power of his own attack, erasure, soul manip, bio manip, transmutation, and every resistance MMX Zero had and maybe even more. I'd honestly back him over MMX Zero stats equalized since his powers are mostly unlimited in use while things like Dark Hold don't last forever.
He should have AP since he is comparable to Omega/Dark Elf fused, both being comparable, and Omega is >> 2.4 kilofoe since he tanked the combined power of X and Zero (who are both >> 1.2 kilofoe since Paradise Lost doesn't even hurt them), while Goku is an unknown amount greater than 4x stronger than Gohan, who is a little above SPC who is 1.053 Kilofoe (I don't buy Gohan being 2x stronger than Cell, since if that was the case Cell shouldn't have been able to break his arm))
Goku's only advantage is flight, but he doesn't really have a way to capitalize on that with terrible stamina, no way to sense Zero if he hides (and he can't just nuke since only one of them can survive in space due to their physiology).
MMZ Zero honestly could solo Buu Saga DBZ