I think the consensus is that you're right on all of the above points. From what I've seen on this forum, most would agree with you. It's a great movie (especially the 2003 cut).
The problem I think is that it wasn't the sequel that anyone wanted. For me, the "we'll get rid of Hicks and Newt in the first scene" just didn't fly. Look, there's all sorts of dramatic reasons why this had to happen for THIS movie -- but I feel that those characters had been so indelibly burned into the consciousness of the fan brigade, to treat them as such really grated.
There's a 50+ page thread on the forum that talks about where the facehugger came from as well - we can postulate all we like with the benefit of hindsight, but this was another "wtf" moment (for me, certainly). I remember sitting in the cinema really excited and coming out feeling really deflated.
Rewatching it on blu-ray and all that certainly gives you a chance to appreciate the film - its just a pity that the director didn't get involved with the commentary (I have to say that I never really enjoy SFX or actor commentaries, they're not my cup of tea) because I would have loved to heard his point of view.
I just thought - maybe it would have flown better if it was the sequel to Alien. Maybe we'd have bought the facehugger being in Ripley's life-raft because, at that time, we had no Queen, so that would have worked. I get that Fincher didn't want to do what Cameron had done (in the same way that Cameron doesn't want to "spend his career cleaning up after Ridley Scott") but I think the whole thing certainly disappointed me. Even when I watched it a couple of weeks ago!
However, it can also be argued that it was, in a way, the perfect ending - "you've been in my life for so long now, I don't remember anything else" - you know, from that perspective, Ripley's story had a beginning, middle and end - its almost operatic in its tragedy.
