"I still think that Scott can make an amazing Alien movie, he just needs a good writer who.....has a backbone strong enough to tell Scott when one of his ideas isn't that great or unique"
In other words, someone who's not afraid to get fired and blackballed?

In all seriousness, no disrespect to Mr. Scott, but he doesn't strike me as the kind of director who will take criticism very well at this stage of his career. Perhaps he thinks that he has made enough successful films and money to know perfectly well what is the best way to proceed all on his own. I don't see Ridley compromising his vision in the future.
"Whatever happened to just wanting a good entry no matter who it came from and where in the timeline it fits."
I can't say with any degree of certainty, but it most likely went the way of Xbox VS PlayStation, Ford vs Chevy, ect. ect. The prequels have created a new level of division. Those that like them, feel we're on the right track. Those that dislike them, feel we've lost years of potentially good Alien films, and the future remains bleak. Regardless of where one lands in that debate, it seems unrealistic to expect we'll ever see a film like the first two again, where they were significantly different in tone and style from each other, yet still managed to deliver a positive experience for a large portion of the fans. Whatever happens from here, it's just out of our hands.
I do hope I get to see an actual Alien film of the older quality at some point in my lifetime though, but I'm not getting my hopes up anymore. And I do think it would be good form to let somebody else make the kind of Alien film for the fans who don't like the prequels. There should be alittle something for everyone at the table.