It's something I've sort of been thinking about as well - that the alien also inherits intelligence & genetic instinct from the host.
If true, every Alien & hive would have different intelligence levels. If "IQ's dropped" while Ripley was away, then the hive at Hadley's Hope would be less intelligent overall.
If Shaw had the highest IQ of the Prometheus crew (like in Spaights' script), then Shaw's "baby" might gain some of her intelligence. Although maybe "it only takes half a brain", and the Trilobyte became more intuitive than intelligent...The goo form of the Alien DNA has the potential to blow people's brains, morph their heads & turn them into mindless zombies. If it's been specifically designed to take intelligence from the head, that might also explain why the head/brain, "tricking the brain", and the trick is "not minding" are so important.
I think it's what's inside the head that counts in terms of the recurring head symbolism. The pancreas is kind of like a second brain in a way. Neurons in the pancreas interact with the brain early in development, and the pancreas is responsible for what we call "gut feelings". Maybe the Alien is more instinctive than intelligent by nature, and it just intuitively/automatically knows things about its surroundings. It can learn & remember, but it's "free of delusions of morality or logic". Driven by instinct. Almost like a subconscious urge. Sometimes displaying MOTHERLY intuition or telepathic communication between the hive (in Aliens). Weyland already knows how the human mind works (and by extension parts of the Engineer brain). They can trick any Engineer or human brain back to life, and can even monitor the subconscious. They need to learn how the Alien's brain works... So Weyland-Yutani can trick one back to life. They can just kill one and reanimate its cells later once they understand more. But nothing ever works as planned...
Shaw had "good survival instincts" "in her". Maybe David was actually trying to give her a compliment when he said he didn't think she had it "in her". Shaw was intelligent & instinctual enough to survive. She managed to create life so she proved she had "half a brain" because anyone with half a brain can create life... Shaw's instincts would be in her 'baby", and could be part of what David was looking for "in her". In the Spaights script David reads all their psych profiles & calls them all stupid. There are different forms of intelligence, though. Maybe Weyland wanted crewmembers who would blindly follow his agenda; or ones who wouldn't ask too many questions. Perhaps the Prometheus crew was selected specifically for their low IQs and manipulability --meaning their ability to be "tricked".
I think Weyland corp has made a habit out of tricking peoples' minds..And that their dreams were being watched so that David could learn how best to manipulate them. Weyland used the "big questions" to get Shaw onboard but he always had his own agenda. He talks about his loose morals and how he's willing to do anythng to get "ahead" in the TEDtalk. David tricks Holloway into agreeing to anything and everything. They're constantly tricking people into dying & brains back to life. Maybe the crew has always been expendible and it all serves some higher purpose to Weyland. Maybe the Prometheus crew were more than expendible. They were almost "sacrificable"..