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.)