Alien: Resurrection was released to mixed and some fairly positive reviews, but over time it has become the outside runt of the litter.

It was Jeunet himself who was the one that was taken the most by surprise. The French film industry works a little different to Hollywood, being a little less about money and a little more about creativity, but Jeunet was trained as a commercial director, and so he was well capable of taking on this job. With a script written by Buffy, Firefly, and Avengers mastermind Joss Whedon that had little to no changes to what ended up on screen. Jeunet quickly assembled a team which comprised mostly of his French crew, presumably for some familiarity and easier workflow.
The team were also seemingly doing things the right way. They really researched the genre and the series itself , with multiple viewings of all three Alien films for inspiration. Jeunet himself even looking at old shooting schedules for Alien and actually attempting to mimic the shot list which Ridley Scott had in place for the first film in order to try and capture some of that flow.
Well, nothing really. Unlike Alien³ there were little to no problems on the shoot. The script was completed well before shooting began, and went through just one or two re-writes, with everyone seemed to get on just fine with each other.
I make no secret of the fact that I'm a HUGE fan of Alien³. I think it's a brilliant, beautiful looking film that is so bleak and unforgiving in the way it ties up the story, which is hugely unexpected, yet so perfect at the same time. It could have been better yes, but the fact that David Fincher managed to do what he did with no script when shooting began, and with all the studio interference he had, I think it's nothing short of a miraculous triumph. To this day, it polarises fans opinions, and while some criticism of the film is entirely justified, trotting out the tired old excuse of "they killed Hicks and Newt" time and time again really just shows that the point of that decision, which was made in order to produce an empathic reaction to Ripley's own sense of despair and nihilism, was well and truly missed.
Studio's being studios they do their thing, but I think by the late 90's the stories of Fincher's troubled time had really been circulating. Considering he'd had a real smash hit with Se7en in 1995 and was becoming one of the hottest directors around, the studio was careful not to pile on the pressure again.
What they did do though was draw up a list of demands that they wanted for the film before shooting began. Jean-Pierre Jeunet has stated in interviews that he was happy to comply with these demands and basically did what they wanted. So with that, although he did get a fair amount of creative control the ship was still being steered by someone other than the captain.

It's main problem is that being 'decent' just isn't enough to carry the weight of the Alien name. Ridley Scott and James Cameron were tyrants with a lot of creative control over their movie. Fincher was a bulldog who steadfastly refused to bow to studio pressure, and so a lot of his genius actually came out on screen. With Jeunet basically painting by numbers, there is next to nothing new in the film.
Being shot entirely in Los Angeles, the film seems to feel disconnected from the previous entries which were all shot in England and used the absolute cream of British craftsman and crews - the spirit of which seems to be sorely missing.
The bottom line is you can't actually do anything new with this series as it's all been covered before. As phenomenal as the Alien saga is, there really is only enough material there to cover the three films, and trying to push it further with the same thing just ends up being repetitive. I mean, how many times is this woman going to wake up and have to deal with these monsters?
The answer, of course, is to show the character of Ripley some respect and leave her in the grave. Her story has been told, and it was a tragic one, but also highly noble too. This doesn't mean than the Xenomorph's themselves can't still go on. (Although with Fox's later attempts I'm not so sure)

Some of the digital effects can seem a bit twee though. 1997 was known as the year of bad CGI, as this was at a time where the technique was becoming more cost efficient to use, but hadn't widely reached a technical level of realism yet. There were a plethora of films in and around that year with some really ropy CGI sequences, the worst offenders being Mortal Kombat: Annihilation and Spawn. Alien: Resurrection does suffer from occasional and obvious PS2 type images, but on the whole they are above average for the time.
So how could it be better?
As stated previously, Ripley just shouldn't be in it. It's not that Sigourney Weaver is bad. Far, far from it (although it's hard to tell just exactly who's side she is on at times), but it's literally crowbarring the character back in to the series just to have her face on the screen, and this isn't the same Ellen Ripley that we all knew and loved from the previous adventures. There are still eggs on LV-426, so the Company/military could have easily gotten some from there and had no need for the clone. The action could focus solely on the crew of The Betty who, as in the film, are delivering a cargo to the space station and get caught up in the madness. They don't need to be picked off one by one either. That's been done - for three films worth, and it could have launched the fact that they perhaps become Alien hunters after this film, with a franchise being built around that.
Another big issue I have with the film is it's sense of taste. Look, I'm no prude. I love a bit of gore and people doing horrible things on screen, but there were parts of Alien: Resurrection that I sort of squinted at. The Newborn creature in particular near the end, which in my opinion almost completely ruined the film. It's grotesque simply for grotesque's sake, plus the fact that it serves absolutely no purpose at all to move the story or characters forward in the film. The actual creature itself was inventive in a few ways, in that it's change of facial expression was rather unnerving. That was good, but how did it serve the film? It didn't. The creature actually had to be dialled back a bit for the final release as it's original design featured a gaping belly chuff and willy combo which was digitally removed in post production. H.R. Giger's original Alien design had subtle hints of sexuality combined with in built fear elements, like a focus on teeth, and a lack of eyes. Simply flinging in a big white skull faced atrocity that goes around mashing people's heads for the hell of it has absolutely no finesse, and it was a terrible way to end the film. Jeunet also seems to be as fond of slime in his film as Ridley Scott is of smoke in his, and a lot of things in this film looked overly shiny and drippy. .
The last 20 minutes or so reminded me a lot of The Fly 2 which was little more than shock and some pretty nasty gore that I didn't care for. David Cronenberg is the master of body horror, and admittedly the first Fly movie gives me the heave, but there was a point to it, and it's a brilliant film nonetheless. Creating some horrible monster that looks like an old woman getting out the bath, and then setting about a series of pretty bloodthirsty deaths before the creature itself is killed (which is shot in a way that descends into nothing more than lowbrow splat) is just cheap film making. As a 'final battle' or climax it's poor indeed. Extreme yes, but it's a dumb bookend, shamelessly plugged into an otherwise enjoyable film which plays to the lowest common denominator of what will probably be a dumb teenage audience.
There's just no point to the thing. It can't lay eggs or reproduce, and so there will be no more like it. Plus, it only lived for about 15 minutes before being offed. Besides, we've already had our big horrible moment in the clone room, which was an excellent sequence that actually served a purpose in developing Ripley 8's character.
Viewing the film now always leaves me feeling a bit grossed out afterwords, and it's not even becasue the gore is severe (I've seen and enjoyed far worse on screen carnage than this), but that it's just there for basically shits and giggles. Whether this was a decision made by Jeunet himself or was one of the studio's demands is anyone's guess.
Fans always complained that Alien³ (or Alien cubed as I like to sometimes call it) didn't pay enough attention to fan service in that it wasn't just more of the same following on from Aliens. Alien: Resurrection is basically what we would have gotten if that had been the case and the series would have ended on the same so-so note that it ended on with this film.
If Fox had made this film but dropped any connection with the Alien franchise in favour of some sort of genetic experiment McGuffin, kept the crew and did something a little less gruesome for the end then it probably would have been one of those solid late 90's popcorn films which due to it's high production values would have garnered quite a cult following. I mean The Mummy was basically an Indiana Jones rip off but it still did very well for itself.
Nearly 20 years on it's still worth a watch as an enjoyable sci-fi flick but one that not only leaves you feeling that it is the weak link in an otherwise exceptional series but also sort of makes you feel kind of uncomfortable coming away from it.