Here's my two cents....
The
Alien franchise is seriously flawed when viewed as a "saga". It's what you get when the main motivation for making another film isn't to add another piece to the pre-conceived puzzle but to milk a profitable concept one more time. That is why it's called a franchise.
To me,
Alien was a wonderful one-off movie... a great haunted house film set in space. I sometimes think it should have stayed that way. It's kind of funny that the basis for all of these continuing sequels is the desire for "The Company" to get their hands on the Alien to use as a weapon... considering that THAT entity was developed in later drafts of the screenplay. Originally, it was the computer on board the Nostromo that wanted to see the crew meld with the Alien to facilitate man's evolving to the next level. That is why the computer is ironically called "Mother". But it was discarded because it resembled HAL's ambitions in 2001 too much. Too bad... I like that idea MUCH better.
But this change gave birth to "the Company"... the all knowing, all powerful (and implausible) group of suits with the misplaced notion that the Alien could be used as a weapon... a chessy plot device if their ever was one. What company would EVER what a weapon that they cannot control... especially a publically held company?
And yes, I think I'm the only person who likes the first film the best. Although it was a fun action film, I thought
Aliens spoiled the concept by the same way most sequels spoil the original films... by the thought that more is better. In the first film, there was only one creature... and that ONE creature was enough to destroy most of a nearly unarmed crew of the Nostromo. But the sequel has the marines fighting hordes of them swatting them like flies (albeit BIG acid bleeding flies) reducing the original power of the creature considerably.
Also a feature of sequels is to introduce something even bigger than what was there before.
Empire did this with Vader's "Super" Stardestroyer that dwarfed the already big Imperial cruisers. I wonder how long the opening sot of
A New Hope would have been if Vader had been chasing the Rebel Blockade Runner with that ride!
SO...
Aliens up the ante with the introduction of the Queen Alien... a creature that goes against the original concept which had the Alien's victims morphing into the eggs rather than having them needing to be laid by some "bigger" Alien.
This franchise isn't the only one whose installments don't really fit easily together to make any real "big picture" sense. My favorite film of all time
Planet of the Apes (which would have made a GREAT one-off film) is part of a soulless franchise born out of the need for the studio hell bent to make more money... whether it destroyed the original concept or not. And as for those continuing
Ape installments, well, lets just say that THAT saga still sets the high mark (or is it the
low mark?) for implausible plot developments for the sake of merely continuing the franchise.
Although the
Highlander saga comes close...fans of that franchise have their own plot holes to jump over as well.
Like
Apes and
Highlander,
Alien was made with no plan or blueprint for any future installments... so any discussion of plot intregrity will be mired by that fact.