While there are plenty of substantial changes (like Shinji doing the fapping directly looking at Asuka, not just in his room) a lot of the cuts are extra exposition that can be deduced or is communicated visually in the final movie(such as Shinji's entry plug ejecting or Gendo remarking that Shinji is now in control of the impact event etc. ), having Misato just completely explain the conspiracy by herself in monologue rather than showing her talking to Hyuuga, Misato telling Shinji that he's got to destroy all the MP EVAs etc.
The manga makes it very clear that Gendo didn't know (and that Fuyutsuki didn't tell him on purpose) but Sadamoto always made it clear that the manga is just his own interpretation, and at the time that he finished his involvement with the main show/franchise was long since over - also, Manga Gendo is pretty different in general.
Now you're asking, "but isn't he doing all this to bring her back precisely cause he doesn't know?"
Not necessarily.
I've always pointed out that he believes in The Plan for its own sake too, ep 25 makes that pretty clear.
He expects to be reunited with her when The Plan is done & is most certainly looking forward to this/ being carried forward by this hope as a strong motivator.
How different were their plans really? They both involved grabbing the S2 engine while SEELE's didn't.
Conversely, what actually happens in EoE seems to be exactly what Yui had planned, third impact included.
Maybe she felt the prophecy could not be averted but a TI that is then immediately undone would "technically fulfill it"
Maybe it was actually impossible & predermination really exists in-universe; Maybe its a result of Yui being brought up in the SEELE cult mindset. Like a protestant would renounce the catholic church but still believe in Jesus & shit.
(As Fuyutsuki asks earlier, "Will [EVA 01] become an ark to save us from the destruction of Third impact?" )
Nor does Yui say much more than "what do you wish for" until AFTER Shinji made his decision. Maybe she didn't care what he picked, or - more likely - she believed that hed act like she expected it in the end.
So maybe the only difference between their plans was that Gendo firmly believed that the resulting conglomerate in the sea of lcl would absolutely decide to stay tanged forever but up to that point they're the same...
well, we know one point where it differs: Shinjis involvement. Yui seemed to have planned that he would be the pilot & insists that he stays the pilot when he considers leaving in ep 19.
Rebuild is a different ballgame but as far as the original series goes, Gendo wasn't planning to have Shinji pilot at all, he only got called cause Rei was out of commission & whenever Shinji thinks of leaving he declares that Rei will now pilot eva 01....
And certainly creating her was not in the original plan, as she is essentially a means for him to do the picking himself instead of how Shinji ends up doing it.
Then there's this bit from the Q&A where we also get the name origins for everyone etc:
(emphasis mine)5.2) What happened to Shinji when he was small? (ep.21)
He witnessed Yui's fatal accident, and "ran away" from NERV and his
father. Probably as a result of this and Yui's death, Rei is
recruited as a pilot. In the earlier episodes he has no recollection
of this. We were made to assume that Gendou abandoned him to work on
his project. Shinji finally remembers in ep.(20? 21?).
I don't think this justifies what Gendou does to his son, but that's a
different question.
Like I mostly took the line in ep 20 to mean that Shinji "ran away" in the sense that the experiment was just frightening to witness & that he blamed Gendo for her death. But you could kinda deduce some implication here that they actually tried to make 4 year old Shinji the pilot. (Asuka wasn't much older after all) Several toddler tantrums later, Gendo sent him off and went to work on the vat with Yui's remains, "Screw it, we'll just Frankenstein us a Pilot."
One might also wonder if he knew this at the time or only found out later(which he probably didn't - he was missing for a week, was said to have changed greatly...)
Or maybe he thought he could handle it all by himself/ was fine with the temporary parting but then quickly found that he couldn't & had no means to manage a grieving, tantrum-throwing toddler.
Of course its possible that the idea that "only Fuyutsuki knew" emerged later in the writing process.
But even in the final version he has a line at the end of the meeting with SEELE (right in front of Gendo) that's somerthinglike "...such is the will of the soul that lives on inside EVA" or something like that. It's vaguer but there's a similar implication to it.
We could end with some Rebuild-related speculation like how The Plan (according to 1.0) seems to have been drafted while Yui yet lived and how in the one flashback we see of her she's telling Gendo to "take care of Shinji" (like she knew she was going away) but at this point the agendas of both of themare complete enigmas & it makes no sense to have this convo when the fourth movie is (hopefully) about to drop in a few months.