It sounds like I both agree and disagree with you on many aspects of the greater Alien universe. I for one disagree with the main question on which is better: Alien or Aliens. For me, that is the most interesting question when dissecting the franchise. I have come to the conclusion that it comes down to being an optimistic person versus a pessimistic person. The easiest metaphor contained in the 2 movies is the manifestation of the cybernetic organism. Ash is bad, Bishop is good. I tend to be a glass half empty guy most of the time so I identify more with the story that says AI would behave in a malevolent way given the opportunity. Part of the reason why I also have a soft spot for Prometheus, although I admit it is not better than Alien 3.
The parts where I agree however are your love for Alien 3. I think the 3rd entry is unfairly maligned because of how amazing the 1st 2 entries were. Also, if you look into the history of the film, it is fairly obvious that David Fincher was not given artistic control over the film. There are a lot of good elements to the film. Dutton’s character Dillon being the best. I also like Morse and the warden’s assistant. Overall, Alien 3 is underrated.