These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
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?
Given how worn down and tired the entire crew occasionally seems in Nemesis, withdrawal actually might explain a lot. Of course, they are also all older than the original series' crew was when they retired.
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.
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.
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.
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...
Growing the Beard: An extremely fitting inversion, as the very beard that inspired the phrase is shaved off right around the point that the entire franchise started to decline.
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: There were much better arguments against The Needs of the Many claim, not in the least bit that the information about the supposed medical benefits they'd get from destroying the Bak'u world as opposed to putting a few million scientists on the other side of the planet and study it that way come from people who are supplying their enemies with materials necessary to their war machine.
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.
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 of mass-kidnapping and invasion of a neutral civilisation as completely reasonable simply because he has a few legal loopholes on his side.
Troi and Crusher's girly girl exclamations about how their boobs are no longer sagging.
Anything Ru'afo does usually qualifies.
Picard's Eureka Moment about the planet's youth-giving properties coming from doing a mambo.
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. No, they didn't want to be forcibly relocated and their planet destroyed. 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 plan A.
Rooting for the Federation: The Federation had very good reasons for trying to force the Bak'u off the planet to study the anomaly. They were also initially trying to get the Bak'u off peacefully, only to have their plans thwarted by the "heroes". Even when they resorted to more drastic measures, they still found nonlethal means to try and remove the Bak'u. See Strawman Has a Point below.
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, they mostly came off 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 (which they may or may not have depending on how the Federation handles squatter's rights), and is in itself wrong, even if it was meant for the greater good of the galaxy. But since the Bak'u are such Jerk Asses for not letting anyone even just study their planet to understand its powers, 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.
If 300 years of living, building and raising families there doesn't give them a "legitimate claim to the planet" (or at least the small area where their village is located), what claim do the Federation supposedly have?
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.
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.
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.
As Linkara pointed out in his review, Captain Picard was willing to do the exact same thing the Federation wanted to do with the Ba'ku to a group of Native Americans in a season seven episode. The Native Americans actually had a better reason than the Ba'ku as they came to the planet specifically not to be moved around by the higher-ups as they had in the past, and unlike the Ba'ku they did enter negotiations willingly and compromised. But since the Ba'ku are white, it's totally permissible for them to claim the whole planet for no other reason than to hog their immortality and refuse to listen to reason, and any attempt to move them is evil.
This argument falls apart when you remember that the Native Americans were human Federation citzens until said compromise, on a planet whose ownership was disputed at the time they landed there, not an unaligned sovereign race who had been on the planet for longer the Federation had even existed.
So, remember when Picard says that with their losses to the Borg and the Dominion, their needed to rebuild their forces, to the point where they are now even letting races that have had warp-capability for a year join the Federation? So in essence, they're using them as Cannon-Fodder?!
More likely they need their resources, by this stage Starfleet has been greatly weakened and their infrastructure has taken a mauling. No need to recruit new races as cannon fodder when every single Klingon is lining up for the chance.
Unintentionally Sympathetic: The Son'a. Despite being "villains," viewers tend to sympathize with them because they're dying and trying cure themselves and because the Ba'ku FORCED them off the planet.