Higurashi implicate a plot reason, Inafune did so twice.
For future reference, let's compile the relevant quotes:
MMXOCW:
*X image with his scarf taking up half the picture, you know the one*
MARKETING ILLUSTRATION
"When I heard the timeframe was set in the year 22XX, I realized it was the same as the Zero series. That's why I added a few touches to give it a bit of a Zero flavor. Initially, I had some reservations about X's design changes, but I think it suits him quite well." (Higurashi)
*****
MM25:
Higurashi: "Command Mission" is technically a spin-off, so even though it takes place in 22XX, it's not necessarily the same "22XX" during which the "Zero" series takes place. Still, we didn't want to cut it off completely just because it's a spin-off. Our goal was to incorporate some of the "Zero" series' flavor in order to make it feel like "Command Mission" is still connected to the other games, like it is part of the same family. So it might be easier if you regard "Command Mission" not as "a story that takes place between X7 and the Zero series", but rather as "one of many potential futures that exists independently from the Zero series".
*****
Sean: Repliroids in Rockman Zero look quite different from the
Repliroids that are in Rockman X. Is there any specific basis for
this change, such as new technology, or is this merely a change of
art style?
Keiji: Of course, yes, Mega Man Zero takes place 100 years after the
X series, so of course the technology has advanced quite a bit, and
we had to redesign all the robots to reflect that.
*****
ibehv: Why is zero's appearance in megaman zero different from his appearance in megaman x?
Inafune: Zero is one of the most important characters for me. Initially, Zero was created for the Mega Man X fans as well as for fans new to the series. But rather than making a game with Zero as a main character in the established storyline, we wanted to create a brand new storyline for him with a completely new game design. Thus, Zero you all know now was born. The story of the Mega Man Zero game also tells you the secret behind the Zero’s appearance change. So if you haven’t played the game yet, please try it out!
*****
In summary:
-Both of Higurashi's statements assess: "22XX" requires some "ZERO-series flavor" (X's new armor,
cutting-edge in-game, is the most prominent example.)
-Inafune does say 'all' robots were redesigned to reflect the advanced technology of 100 years later. (No distinction is made between combat and civilian models.)
-The 'story' reveals a 'secret' related to Zero's appearance change. (Weil's quote about Omega being the Original Zero which he upgraded applies, see below.)
Because outside of the missing Z-Buster which the X-series itself has no problem with, there is absolutely no documentation that Zero's body was modified prior to his first seal. Omega's origins dictate that Zero's original body was taken prior to the start of Elf Wars, therefore it speaks against any such body redesigns being Elf Wars-centric, barring Weil and Ciel's grandmother stealing each other's designs, anyway.
Lacking both the Triple/Chain/Recoil Rod and Shield Boomerang, while having the Rock Buster Mk.17 enhanced Z-Saber with bustershot, we confirm upgrades to the original Zero's arsenal while at the research institute (mind and body separated, weapons expert Dr. Weil involved). The magazine clip functionality at least informs us of intent to replace Zero's old Z-Buster and improve his combat performance.
That said, I'd like to present the following quotes:
MMZOCW, Page 55:Sketches of Omega's first form. It is indicated here that the armor covering the body has a dampening effect to contain the overwhelming power within.
*****
ZERO3 Kanzen Kouryakubon, page 131.Zero's defeated the giant Omega, but the strongest enemy now draws near!!
*****
ZERO3:Dr. Weil: Hehehehe... You thought you were a hero all along, didn't you! Never suspecting that you were a mere copy. What a joke! Omega himself is the one and only, original Zero! You're just a copy of him!
Zero: The original Zero... Why is he your slave, then?
Dr. Weil: Hmph! He's a bloodthirsty God of Destruction. All I did was upgrade him to draw out all his power! All right, Omega...... or should I say "Original Zero"! Time to wake this pitiful fake from a century-long deam!*****
Since Omega form 1 is artificially limited in power (Dark Elf being the source of power for the giant Omega / Omega form 2), Weil's quote of upgrading to 'drawn out all his power' can only apply to the original Zero / Omega form 3.
At least two Zero-series mechaniloids already appear in the Rockman Online trailers.
Yes,
Mega Scorpia and
Quicksand Mixer have appeared in Rockman Online (with minimal design changes!). Nothing excludes these mechaniloids from appearing in a parallel universe timeline branch.
That's making a leap of faith on what the intent behind Cinnamon's visions was.
Notice key ZERO-series details are absent from RMO profiles?
X is a legendary Irregular Hunter who worked to destroy the Sigma Virus, which causes destructive behavior in a repliroid, turning it into an Irregular.
He eventually won his battle against the Sigma Virus, and after confirming the world was in peace, went to eternal rest.
For ages, mankind and repliroids believed that the Sigma Virus had been completely eradicated.
Zero is the masterpiece of Dr. Wily, who tried to use Humaroids (humanoid robots) to take over the world.
Zero is known to be the the original host of the Sigma Virus, which turns repliroids into Irregulars, and openly acknowledges that fact himself.
However, despite that dark past, Zero defeated countless irregulars with his undying belief in what’s right, and always trusted the sometimes unsure X, supporting him by his side.Posted on: October 09, 2013, 01:19:05 PM
Relevant addition:
Q.まずはデザインのコンセプトについてお聞きしました。
ロックマンXのゼロをベースにしているのかな?と思いきや・・・
A.Xoverの世界観でいうと、Xシリーズとゼロシリーズ両方のゼロが
混在していると思うので、それらを見たコサックが自身の観点・
Apparently it says that Cossack (in-universe) saw both X-series Zero and ZERO-series Zero, and fused their designs to create Over-Z. Guess they look different after all?