Ritsuko meets Misato and Shinji in a hall instead of an elevator.

Gendo, not Ritsuko, tells Shinji that he is going to pilot Unit-01.

Misato does not give her lecture to Shinji here, as in the anime...

Gendo speaks with Rei at the cage, not through the intercom.

The manga sticks to the term 'Third Children' when referring to the pilots. Seems to have no basis whatsoever in the anime.

Notice that Shinji offers a different reason when refusing from piloting the EVA to battle. In the anime, he "just can't" but here he about admits that it is because he hates his father, Gendo.

Shinji is not in danger of getting crushed by debris. Unit-01 does not exhibit strange behavior (spontaneous activation) as in the anime.

...Misato gives her lecture to Shinji here.

Shinji's "I mustn't run away"-mantra is not used here.

Shinji's main reason for piloting the EVA is he doesn't want to let his father call him a coward.

Misato notes that the Angel had predicted their actions.

Instead of falling down after the first step, Shinji cannot stop the EVA and charges at the Angel instead. The end result, however, is same as in the anime: all contact is lost with unit-01 and it doesn't respond to any commands.

Compared to the anime Shinji exhibits drastically different behavior. In no way he is a wimp, foolhardy is the more appropriate word...

Evidently the Angel has an ability to track the Eva's location. This conclusion can be drawn from the anime as well, it is told here with greater emphasis.

As Shinji lays unconscious inside the EVA, he has a vision of his mother which turns into the EVA (without the armor that covers her).

The battle between the berserk Unit-01 and Sachiel is told here, not later as in the anime.

The scene where Shinji sees the unmasked EVA face has been left out, probably because he already saw it in his 'dream'.

What?! Sachiel's AT field is... hexagonal! Also note that later (on stage 16) Ramiel uses an octagonal field.

The scene in the beginning of this stage is very interesting. It foreshadows future revelations about the Evangelion Unit-01.

Notice Gendo's smug face as the Evangelion goes berserk. As if he had expected that to happen... But yes, in the anime Fuyutski comments "We've done it!" when the unit goes berserk.

Why Sachiel self-destructs? It is the only Angel which decides to die that way... and it should be well aware that it cannot hurt the EVA with the explosion.

Shinji has another dream of Unit-01

Apparently, he suffers no memory losses.

The meeting chamber of the I.P. Committee looks different.

Gendo and Shinji meet in the hallway, not at the elevator. Shinji sees him talking with Rei but ignoring him. As a personal note, I though the anime's elevator scene much more... intense.

Shinji has an argument with Misato at the hospital. She decides to take Shinji to live at her place to 'fix his personality'.

The 'homecoming scene' from the anime is missing. No Pen-Pen, no toothpicks and stuff.

The SEELE member refers to an "Intel op". I guess this is the same as the publicity control scenario they discuss in the anime, as Gendo's answer to the question is the same ("It has already been taken care of.")

Looking back at the six first stages, Sadamoto has cut away the 'fan service' and some of the humor of the series. Perhaps he intends to tell a more serious story. On the other hand, he offers a bit clearer motivations for some characters, especially Shinji.