We honestly don't know what the effects of the metaphasic radiation has long term. While its kept the Ba'ku alive for over 300 years, we also know that it increases metabolism, energy levels and youthful feelings from those affected. Hell, that was even a concern in the film, how much it was affecting the Enterprise crew's rationality! What exactly is there to say that the Son'a, once deprived of this, eventually suffered massive withdrawal symptoms? And while 80 years of normal aging clearly has affected them, they constantly have to undergo medical procedures and blood toxin filtering, despite not seeming to be either infirm nor decrepit beforehand. After 300 years of exposure, who's to say that the real reason they have such Body Horror is because the radiation simply destroyed their bodies natural ability to function and they are simply rapidly decaying without it?
The Son'a are mentioned as having no issue with taking slaves. Come to think of it, for a society that has rejected the washing machine and the vacuum cleaner, the Ba'ku settlement is remarkably clean, don't you think? After all, it's heavily implied they've got a large stash of technology lying around somewhere, how about in that massive system of caves? What else might they be hiding?
Anvilicious: Picard's monologues in which he speaks of forced relocation in human history, both with Anij and Admiral Dougherty.
The Son'a, a race whose hat is being overly tanned, getting too many facelifts and dealing drugs, are an incredibly unsubtle satire of people from Los Angeles.
It caused an additional problem for non-US viewers as well — the UK, for instance, was only about halfway through the show's fifth season when the film came out, but the film made references to stuff that happened in the seventh season.
Few people can deny that this is one of Jerry Goldsmith's best soundtracks in the franchise.
Designated Hero: The Bak'u. The movie perches how perfect they and we're supposed to draw parallels between them and native Americans that endured genocide from the US government, but as pointed out below, they are hogging the planet's radiation that could save billions of lives just because they don't want to be inconvenienced. And, as pointed out by SF Debris, the only reason for the forced relocation is that if Starfleet and the Son'a went to them honestly and ask for their cooperation and they refused, choosing immortality over helping save countless lives, then they would have become the villains of the story.
Picard even defends them by saying that "Forced Relocations have destroyed cultures whenever they have happened throughout history," which is rather seriously undermined when you remember he has taken part in at least two forced relocations in his own career, including one against a planet full of Native Americans, as was pointed out by Linkara in the Nostalgia Critic's review of the movie.
This isn't as hypocritical as it's commonly made out to be though. Both of those relocations involved colonies of Federation citizens on a planet that had legally become the property of a potentially hostile foreign power, not colonies set up by a neutral party on a planet that the Federation is only now claiming authority over for their own benefit.
This is just hair splitting. On the other hand, Dougherty's actions were intended to acquire life-saving technology which would have saved billions of people during a massive war for the federation's survival, whereas Picard's were intended to appease a morally repulsive dictatorship which had no desire for peace with the Federation and which they immediately violated by basically committing genocide on the remaining inhabitants (Picard did nothing about this, and in fact took the side against them). And the fact remains that none of the arguments presented by Picard in this movie do not apply equally to his own previous actions.
Designated Villain: The Son'a, and to a lesser extent, Admiral Dougherty. As brought up below, what they are doing will save billions, and the viewer is supposed to draw parallels between them and people that wrought genocide on the Native Americans through relocation, but what they're doing removes the Bak'u non-violently and the Son'a only resort to violence as a last resort, and they're doing all this because they'll all DIE if they don't.
Esoteric Happy Ending: The movie ends with theBak'u welcoming the Son'a(who are banished Bak'u) into their society and allowing them to keep their planet and its fountain-of-youth powers. Except that it was pointed out that it will take ten years for the planet's rejuvenating effects to really affect the Son'a, and many will not make it that long. Plus, the Bak'u will maintain their monopoly on rejuvenating powers which would certainly benefit billions across the galaxy.
Billions, mind you, that will almost certainly die without the medical technology, as the Federation is in the middle of a war with the Dominion and Cardassians, who outnumber and outgun the Federation, Romulans, and the Klingons combined. So, the thousands- if not millions- who die in the war who could have been saved after being shot by the Jem'Hadar by the medical techniques and technology developed by studying the healing energy? They can die easy, knowing that the thousand or so Ba'Ku/So'na are going to be all right.
It should be noted that the top So'na are revenge-driven jerks who are allied with the Dominion, so destroying the fountain of youth planet based on their word might not be the best Plan A.
Everyone Is Jesus in Purgatory: In this film, Picard is essentially playing Moses, with Admiral Dougherty leading the Philistines. Marina Sirtis joked about this on set.
And the more conventional Aesop about the planet's rejuvenating powers: "Finders keepers, losers weepers".
Hey, remember Spock's extremely sad, moving line about how "The needs of the many outweigh the needs of the few?" Turns out that "the many" are called "The Ba'ku" and "The Few" is anyone else who wants to use their planet's healing powers, which is... several hundred billion people... who will probably die in the massive war that is overwhelming all the other powers in the Alpha Quadrent combined...
Hilarious in Hindsight: Brent Spiner wanted Data killed off, but was overruled. Reportedly, his script came with a note reading "Better luck next time." Well...
Idiot Plot: The plot itself breaks down immediately due to the fact that there are only about 600 Ba'ku, living in a single village, with no advanced technology. This makes the entire plot a glaring case of Sci-Fi Writers Have No Sense of Scale, as it is never explained why the Son'a had not simply taken up regular residence someplace else on the planet decades earlier. There was no indication of how the Ba'ku could have forced them to remain offworld, even if they were not welcome in the community. Likewise, the Federation could have established entire cities elsewhere on the planet, thousands of miles away from the Ba'ku village, without them ever even knowing!
The concept of using one of the most iconic technologies in Star Trek, the Transporter, to simply beam Data to a secure location once he starts going crazy would have prevented the entire plot from happening.
Inferred Holocaust: Even though they've been welcomed back by the Ba'ku, the Son'a will likely die out in the next few years, as Dougherty pointed out it would take 10 years of normal exposure to the planet's rejuvenating radiation to help them, and most will not make it that long.
A more subtle one, but without the potential advances in healing technology that the planet's radiation could provide, the casualties of the Dominion War that was ongoing at the time were probably worse.
It's the Same, Now It Sucks: While overshadowed by certain other complaints found here, another major one is that the film feels like little more than an episode of TNG, which is doubtlessly a consequence of writer Michael Pillar having worked exclusively in television before this. Insurrection would end up being the only feature film he ever wrote.
Mary Sue Topia: The Bak'u, who live on a planet with fountain-of-youth powers and espouse a technology-free society. They still use all pre-industrial technology though, making them not as "primitive" as they'd like to claim. SF Debris tore them apart in his review, pointing out how improbably clean and orderly everything and everyone is, especially since our modern standards of cleanliness are derived from technological advancements.
Misaimed Fandom: While Dougherty's motives are ultimately sympathetic, it's rather disconcerting for some that so many fans of the franchise see his plans - i.e., invading an occupied planet, kidnapping the entire population and stealing its resources in a way that will make the planet uninhabitable, and possibly completely destroying whatever made the resource so valuable in the first place - as completely reasonable simply because he has a couple of legal loopholes on his side.
Not even the fountain of youth can bring Picard's hair back.
Ron the Death Eater: A lot of people found the Ba'ku repugnant because they didn't want to share the medical benefits their planet could provide. Supposedly they're preventing medical benefits that could save billions of lives from the Dominion, but considering the people who came up with the "destroy the planet" plan worked with the Dominion, maybe trusting them at their word isn't the best idea.
Rooting for the Federation: The Federation are considered by many (including some members of the cast) to have had very good reasons for trying to force the Bak'u off the planet to study the anomaly, and they were consistently willing to use non-lethal methods to do so. See Strawman Has a Point below.
So Okay, It's Average: Of all the "bad" Star Trek films, perhaps the one that has the fewest defenders or detractors, on account of being so ineffectual and forgettable. SF Debris sums up popular opinion quite succinctly:
It isn't loved like Two, popular like Four, prescient like Six, exciting like Eight. It doesn't have people rushing to defend it, saying it's cerebral like One, significant like Three, ambitious like Five, landmark like Seven, or theatrical like Ten. Insurrection stands alone: bad enough to be hated, but not bad enough to be loved.
Special Effect Failure: ILM didn't come back for this film (in part due to being busy on The Phantom Menace, though Rick Berman said at the time that he wouldn't have hired them anyway, since he felt other FX houses could provide the same quality for cheaper) and the quality of visual effects suffered a major drop as a result. The effects aren't terrible for the most part, but they were considerably behind even what other film were doing with CGI in 1998.
The hummingbird seen during the slowed time scene looks really horrible.
The fight scene in the projector, where they just left the bluescreen in instead of chroma-keying whatever was supposed to be there.
Squick: Dougherty's murder is one of the more graphic in the Star Trek mythos. Death by skin stretching.
Strawman Has a Point: Shouldn't the needs of the many outweigh the needs of the few? While the Bak'u were supposed to come off as innocent victims of an under-the-table Federation plot to steal their planet's resources, viewers tend to interpret them as selfish pricks who won't share (or tolerate anyone of their own who wanted to share) their planet's amazing power of healing, leaving the rest of the galaxy to die of diseases they themselves easily overcame. Of course, the idea of a land grab from them greatly violates their rightful sovereignty, and is in itself wrong, even if it was meant for the greater good of the galaxy. But since the Bak'u are interpreted as such Jerk Asses for not being willing to give up their homes to allow the radiation to be collected and distributed, it's hard for some to feel sympathy for them.
Also, the Bak'u don't really have a legitimate claim to the planet. They were just refugees who just happened to crash land on the planet and decided to eliminate all their technology, fooling the Federation into thinking that they were a pre-Warp civilization. Not that the Federation's claim is any better.
Admiral Dougherty makes a point that many viewers considered a better argument than the writers did:
Dougherty: They are not indigenous to this world, they were never meant to be immortal!
Though this ignores the point that a significant number of the Ba'ku were born on the planet.... Though by that logic all of the Son'a were also born on the planet and were forced to leave by the Bak'u due to ideological differences.
And there are only like 600 Bak'u on the entire planet. Most small towns have more people than that.
And worse, as many have pointed out, this movie takes place during the Dominion War, and the medical technology that could have been developed from the planet's energies might have helped give the Alpha Quadrant races a distinct advantage. Also, once the Dominion found out about the planet (as their excellent espionage would have almost certainly allowed them to do) they would not have hesitated to obliterate the Ba'ku and take the planet for themselves. Ironically, the only thing likely to save the Ba'ku from such a fate would be the Federation!
They Wasted a Perfectly Good Plot: The original script had Data apparently going berserk and Picard tracking him down and terminating him, only to find out afterward that Data was right, but Patrick Stewart wouldn't go for it.
There's also the basic fact that the movie took place during the Dominion War, and the Enterprise is one of the most advanced and powerful starships in the Federation fleet. And instead of showing the Enterprise out on the front line... This.
At least one extended universe novel handwaves the Enterprise going in the opposite direction of the war for plot purposes by stating that it and the crew are just as high-profile in-universe as they are to the viewers, if not moreso, and thus they can't be deployed to the front lines for fear of inspiring the Dominion to throw a completely disproportionate response at whatever force its assigned to (unfortunately, why no one thinks to use this to bait the Dominion into an ambush or at least an unwise engagement is not covered.) Or just move the crew to another ship for their diplomatic work and put the flagship back in the fight.
The Federation were currently operating in a time of war against the Dominion and they are losing. More than one reviewer has noted that it wouldn't have been too hard to have the crew become divided over whether removing 600 people to potentially save billions is the morally right option (SF Debris in fact suggested this as a better alternative. He especially thought it was incredible Geordi would be so blase about giving up his natural sight).
Unintentionally Sympathetic: The Son'a. Despite being "villains," viewers tend to sympathize with them because they're dying and trying to cure themselves.
Unintentionally Unsympathetic: The Ba'ku, to the point where some viewers argue they deserve to die. At the very least they come across as unbelievably self-righteous, especially since they boast about understanding advanced technology (like Data's positronic brain) and merely sniff disdainfully at others who actually use such things.
Wangst: Ru'afo basically spends the whole movie doing nothing but whining and complaining.