Great points. I felt the same way with the mind wipe, that was the one thing that strained believability. I get the point in that the conversation needs to end with Wendy/Marcy realizing that Neverland ain't all it's cracked up to be but I think they could have reached that point by having the Dame Sylva wiping Nibs memory, show the Lost Boys gathered together where they learn that Nibs "got sick" and needed to be treated and then later on, Wendy talks to Nibs and realizes that not only has her memory been wiped but some of her abilities (whatever they said to dial down with her settings) have been messed with. Upon learning that, then she starts to question Neverland being a "yes" place.
Huh.
Okay, I may have read that wrong ... but I didn't view that necessarily as Wendy coming to a realization about Neverland. I read that conversation about Wendy coming to a realization about humans.
I'll go back my original post on this being more of a riff on Ridley's Scott's oeuvre in general (and Bladerunner) than Alien specifically. The theme I see running through is the nature of humanity- and how Synths, Cyborgs, and Hybrids are viewing themselves, and viewing their relationships with humanity.
Wendy was raised by two parents- Dame Sylva and Kirsh. A human and a synth. It seems clear that Kirsh's ... worldview is winning out. For now, at least.
(I'd also throw in the prophetic early scene with Wendy and Kirsch watching the scorpion trapped in the glass, and the payoff later (with Wendy watching the alien behind the glass).
IMO, YMMV, etc.