@Huggs, you've made some good points.
And now you've started to address the final confrontation scene between David and Daniels, which I've also believed to be very unsatisfying. It lasts seconds, when it really should be far more protracted to give the audience a bigger sense of a final showdown between the two main adversaries. Like Ripley vs xeno in the Narcissus in Alien, Ripley in powerloader vs Alien Queen in Aliens, Ripley's suicide in the leadworks in Alien 3, and so on, like so many other action movies. It's really an obligatory part of the genre (Arnold vs Predator, McClane vs Hans Gruber, I could go on and on...),
David and Daniels do have their moment together when they duke it out in the temple in the second act. This scene should have been transposed into the climax of the third act somehow. Instead we get a big action sequence between Daniels and the xeno (which I thought was quite well done btw, even if the xeno's demise was a little bit unimaginative), but the xeno - or any of its variants - are not really the chief antagonist. That honour belongs to David. We need a big scene, a significant scene - David vs Daniels, right there at the end.
Your idea for an Alien '79 motion-tracker-dots-in-the-vents homage would have done this. But I think they really need to be face to face.
Here's an idea: Daniels makes it back to "pretend-Walter" to thank him for his help in expelling the xeno. "Walter" needs to hook himself up to a computer for a maintenance checkup and goes into sleep mode. Daniels, in gratitude for his help, tends to his external injuries and sees the wound under his chin (from her nail attack, earlier) and realises he is really David. David wakes up and finds himself manacled to the bench. Daniels challenges him, she knows his real identity, and now his goose is cooked. David resigns himself to his fate and spills the beans about his deranged motives. Daniels is about to kill him when he regurgitates the little facehuggers onto the manacles, squashes them, and the acid releases the manacles. David is now free to overpower Daniels, turning the tables on her. She wakes up trapped in a cryotube. Or something like that.
TC