Everything Giger does is vaguely or overtly sexual. Just look at the derelict! Look at the shape of the...orifices they enter through.
Originally, in the Narcissus, the alien was going to look Ripley up and down in the closet she ran into with the spacesuits. Instead, they had him sit there and slowly and deliberately extend and retract his tongue. How can that NOT be seen that way?
I think many people overlooked that aspect of it on seeing it the first time because of the effectiveness of the terror and shocking violence of some scenes, but you can't see the film 3 or 4 times and fail to pick up on it.
There is one egregious deletion IMO. When Ripley goes to Mu-thur and gets the message that the crew is expendable and Ash shows up (it's Ash, read the credits, no E) she flips out, throws him against the wall, then runs out. Next scene, she has a bloody nose and he's got milk leaking down his head...there was an intermediate scene in the hall outside Mu-thur's room where Ash attacked Ripley and she hit him over the head with something. Without that, it's like she got a nosebleed from nowhere and he's started sweating milk.
The Jedi Master