Original Episode I:
-Episode I trailers have scenes all the way up to Jin & Margulis' sword fight in Labyrinthos including several cut scenes and quotes that never appeared in any sequels.
-MOMO's analysis is almost the same except originally, it was not Juli's idea to destroy MOMO's memory, but a subcommitteeman's.
-The Omega System and the scenes inside were not in the original script. In the original script there was another scene referred to by Soraya as Jr. & Albedo vs U-DO vs KOS-MOS 3rd armament and an antimatter annihilation of Albedo.
-In the original script we saw the death of Sakura.
-Albedo's verbal abuse/violent acts against Sakura were not in the original script and neither was Albedo's quotes; "You look like you just lost your best friend Rubedo..." and "What are you talking about, I can't stand you or Nigredo." among other things.
Original Episode II:
-In the original script Ziggy's past history was an encephalon experience playing out like Xenosaga: Pied Piper (without the rewrites near the end) and subsequently Wilhelm, chaos, Patriarch Sergius, Voyager and Dmitri Yuriev's backstories would've been fleshed out.
-Jr would've rapidly been growing to adult form in the original script and there would be an option to play as either young or adult Rubedo in battle.
-According to the 'leaked documents' (leaked spoilers pre-Episode I) Nephilim would grow into adult by this episode (probably like she does at the end of the current Episode III.)
Original Episode III:
The original Episode III would've been the beginning of an entirely new story arc with a new cast taking place thousands of years later. Most likely it would've played out on Lost Jerusalem 10,000 years later and explored the genesis of humanity on Earth and the beginnings of our local Dimensional Universe. Reincarnations of Jin, chaos, Mary, Abel and Nephilim would've been highly likely to appear.
Original Episode IV:
The original Episode IV would've been the continuation of Episode III and the conclusion of this second story arc. Together Episode III and IV would've replaced Xenogears Episode II-V in the Xenoverse with this new canon.
Original Episode V:
The original Episode V would've been the beginning of the last story arc taking place thousands of years after Episode III/IV and would begin to explore the end of our local Dimensional Universe.
Original Episode VI:
The original Episode VI would've been the continuation of Episode V and the conclusion of the third and final story arc - a.k.a. "the end of the universe" as Takahashi put it.
