Fox's mismanagement of the Alien saga has been legendary from the Alien Vs. Predator experiment almost killing both franchises to producers micro-managing/rushing sequels. The squandered potential of Alien 3 is the most well-known which James Cameron had wanted to make but ended up going on without him. Leading to the studio killing all the main characters even though they would pursue a fourth film. Joss Whedon was hired to script the film while the studio would hire French director Jean-Pierre Jeunet who at the time didn't speak of word of English. Fans believe the lost in translation between the cast, writer and director helped it's poor reception.
Some of the problems on the set of Alien Resurrection include Fox slashing the budget and studio space State-side was hard to find as well. Productions such as Titanic, Starship Troopers and Jurassic Park: The Lost World made it hard for Fox to build the sets needed, leading to sets being scaled back. Resurrection was the only Alien film to be shot outside of the UK. Weaver wanted the film shot in the States because she didn't want to travel. A bunch of producers acting as writers along with off-toned moments ended up giving us one of the worst films in the series. Jean-Pierre also made on the spot changes and removed the original tounge-and-cheek humor from Whedon's script. Apparently, the studio had some high caliber directors on their wish-list who could have been a saving grace for the messy production.
Before making Oscar caliber features such as Slumdog Millionaire and 127 Hours director Danny Boyle had been in the running to direct the follow up to David Fincher's Alien 3. The project would have been Boyle's next film after the hugely successful Trainspotting which put the director on the map. Danny would instead make his alternative romantic comedy A Life Less Ordinary instead. He would later jump into the science fiction thriller arena with films such as 28 Days Later and Sunshine which were clearly influenced by the first two Alien films.
Boyle was the producer's top choice along with other contenders David Cronenberg, Peter Jackson and Bryan Singer (Usual Suspects). Peter declined involvement because of lack of enthusiasm for the film while it's unknown why Singer and Cronenberg passed. Jackson would go on to make The Frighteners/Lord of The Rings and Singer instead made Apt Pupil but came back to Fox to make X-Men.
The supporting cast would have had some comedy and action icons. Dr. Wren had been written by Joss Whedon with Bill Murray in mind and Christie had been a role written for Chow Yun Fat (Hard Boiled, The Killer) both actors declined the film.
Originally, the clone was going to be that of Newt which would allow the franchise to move along without Ripley. The reason being at the time Sigourney wasn't interested in another film. This was later changed when Sigourney Weaver signed on to the film for $11m. Weaver along with James Cameron would try to put the wheels in motion for the fifth film that ultimately never happened. Oddly enough, James Cameron's purposed Alien 3 would have had involved Newt and Hicks. Instead the studio decided to kill them off which still upsets Cameron. Along with killing Ripley at the end of Alien 3 the story choices ended up painting the studio in a corner when trying to come up how to make the fourth installment.
Another creative change was to the newborn which Whedon had written as a deadly four-legged, eyeless, bone-white creature with red veins running along the sides of its head. It had an inner jaw, similar to the all the other aliens. It also had a pair of pincers on the sides of his head. These pincers were used to hold its prey still as it drained the prey of blood with its inner jaw. The creature was also larger, nearly the size of the queen alien. In later script revisions, the creature was changed into a "more believable" hybrid of human and alien. The original newborn's pale apparence seemingly helped influence some of the creature designs on Prometheus.
I have to assume this creature also made it into David Twohy's version of the script and influenced his alien creatures in Pitch Black. Minus of course those aliens were also able to fly. There has been speculation that David Twohy's Riddick franchise was started from the rejected script.
The final act was originally going to be set on Earth but that was given the axe when Weaver disagreed with that direction. A few large scaled action scenes were going to be Earthbound. In the director's cut of Alien Resurrection we get to see Ripley finally on Earth looking over Paris.
The crew of the Betty would eventually give Joss Whedon the idea for his Firefly series which also focused on a group of space pirates.