After the X Series, Zero was transferred into the body that we see in the Zero series as his X series body was studied. Weil stole that body and used it for Omega, and Zero was put in a copy body of his Zero era body.

My head-canon says that prior to Omega's battle with Zero, Weil modified Zero's original body to be more like "copy" Zero's body so that he'd have the strengths of the original body *and* the strengths of Zero's new body. Even so, it's still Zero's original body, just modified additionally by Dr. Weil. In the past, during the Elf Wars, my thinking is that Omega looked like X series Zero, whereas MegaMan Zero still looks like how he does in the Mega Man Zero games. But again, that's just my head-canon.