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"In other words he thought that the Engineers were immortal which they aren’t."

Yes very good point, so when David was preparing Weyland for his journey to meet these Gods, that Weyland was looking forwards to... David already knew they was not Gods and Mortal and if the Engineers where Mortal After All, David knew they could not give Weyland the Gift he desired anyway.

But as David said "does everyone not want their Parents Dead" and so David had led Weyland to his Death?

"I doubt that he would be able to pull of a big plan like that all by himself or totally in secret since the plan is too huge."

Maybe not if David starts to understand the Black Goo, or Xenomorph, if there is a way to wipe out Mankind and leave only Androids maybe the Xeno or related Biology could be part of Davids plan..

Could he end up being the one pulling the strings at the company in the Franchise?

As far as Shaw....

We know Rappace is not cast, but Ridley only said as far as shooting on the movie...  remember he said before that she played a MINOR Role....

Rappace during a interview seemed coy to answer anything but her Face seemed to let on that she knows more than she is letting on and could indeed play a role in the Movie.

This means One of Two Things....

1) They may have Shot Scenes for the movie a while back, maybe a long while back and so she wont join Fassbender and the rest of the cast for Shooting the Movie as any scenes she was in had already been Shot!

2) Shaw is in the Movie so to speak, but Rappace is not, and so we could see Shaw as merely a Prop..

Prop Work for Davids Head..

These were used for when the Engineer hit Weyland and also when Shaw put the Head in the Bag.

This is the Engineer Chest Buster Deacon Scene Prop..

The above shows you can make Life Like Replicas and so my point is a Sleep in Cryo Stasis Shaw that is then used only as part of a Chest Buster Prop would not need Rappace to even be cast at all... only cast being as far as a Mold..

I think something like this could be what we shall see, or at least see something in her likeness... if we just see a Egg Morph or a Hybrid Monster that has no resemblance to Rappace, then maybe we wont connect to her or the comment she plays a minor role.