
Tell me that you didn't wish that the difference in design was a plot point instead of being handwaved as just an art shift. 
Thats badass.
It wasnt ENTIRELY an art shift though, mind you. I mean, do note that Omega uses a gun like Zero's, despite Zero's gun not being an original weapon of his, but picked up from a dead resistance fighter and equipped with the saber as it's magazine. Omega's gun, furthermore, is not the same as Zero's, and was actually completely re-sprited so that he holds it
gangsta style sideways.
Similarly he has plenty of unique animations and sprites. It seems more likely that either
A: Zero's body was upgraded during his sleep and the copy body was modeled after that, thus thats why Omega looks like that,
or
B: Weil modified the body to resemble Zero's more to screw with him.
There was always a theme of technological progression. X himself in Command Mission got a new look because the artist thought that since it was 22XX, that it was the Zero series time.
so while Art shift is a factor, it's hard to tell how much is art shift and how much is just progression of technology. Keep in mind, both X and Zero's technology was fully cracked some time before the Elf wars, during the 50 years that scientists studied Zero's body and mind.
BTW Vlad, where did you find that? It looks like it could be done by the Zero series artist himself. Is it?