The reason the Doctor is so anti-social in early seasons is because his personality was based on his creator, Lewis Zimmerman, who is misanthropic at the best of times. Having Reg Barclay, a Starfleet officer with low self-confidence issues be the Beta-Tester for his personality probably didn't help.
Also remember that aside from Kes the entire crew treats the Doctor as a tool for the first couple seasons, no more worth consideration than a tricorder, as Kes puts it "they treat him like he's not there". It's a perfect reason to be anti-social when nobody gives a damn about you. While this attitude lets up somewhat as the episodes go by, it isn't until the Doctor gets his mobile emitter and fully starts functioning as a full member of the crew, going on away missions, forming friendships and so forth that everybody starts treating him as a real person and thus the Doctor's anti-social behavior stops.
At the end of "Body and Soul" the EMH tells Captain Ranek (who was previously unaware that Seven of Nine was under The Doctor's control) that there are plenty of women out there who'd be attracted to him (looking over at Ranek's attractive female colleague Jaryn as he does to drop a hint), but "I'm just not one of them." Later, when Jaryn points out that she's going to have to rescind that offer she made to him (in Seven of Nine's body) to introduce him to her brother, as he's not exactly her brother's type, The Doctor then wisecracks: "...because I'm a... hologram?" These lines are every bit as humorous as they're meant to be, but seeing how successfully The Doctor managed to counterfeit other members of Voyager's crew, both male and female, in "Renaissance Man" a few episodes later reminds us that he isn't entirely joking. In fact, if he had any ordinary heterosexual guy as a Love Interest, The Doctor could easily change himself into a woman to accommodate the man's romantic desires; he just doesn't want to do that because his mind (based on his creator Lewis Zimmerman) is a wholly heterosexual human male's and he's not into gender-bending.
He's not into gender-bending yet, anyway; since he's well-nigh immortal and likely to outlive a lot of lovers, though, there's no telling what kinds of romantic interests he might develop several millennia in the future or how many various species and sexes he might try emulating in pursuit of these interests.
After nearly 200 years of the Enterprise being "the only ship in range" to defend Earth against a multitude of threats, Starfleet suddenly has 27 ships to throw at the Borg transwarp aperture which Voyager opens up in the finale. It's highly likely that the Dominion War is responsible for this.
There are shipyards at Earth and Mars. After Borg attacks and the war with the Dominion, Starfleet probably had them working at full-capacity to build new ships. At least one Prometheus class ship was among the fleet that was there when Voyager arrived. Since that was a brand new class, it definitely reinforces the implication that some of those ships were fresh from the shipyards, either new construction or having been refitted.
Near the middle of the third season Voyager encounters the Nekrit Expanse, a vast nebular region where ships vanish without a trace and nobody dares explore, a sort of "here be dragons" part of the delta quadrant map that Neelix and the local species know nothing about. The episode ends with the crew bravely continuing through it, without ever overtly explaining why it's so bad. But what does Voyager run into just a few episodes later? The Borg. The Nekrit Expanse marks the edge of Borg space.
Seven's attraction to Chakotay actually makes sense, given that she became interested in him in season Seven, the season where she was generally interested in becoming more human. Chakotay, with his nature-loving and emotional personality, is possibly the most un-Borg person on Voyager.
Chakotay was also the first to connect to her human side, being the one who linked to her mind in Scorpion Part 2 and severed her from the Collective. Does that make this a delayed Rescue Romance?
Her interest in him also only arises after the males she'd be most compatible with are officially off the table. Tom is Happily Married to Torres and Tuvok has a loving wife of his own eagerly awaiting his return, Harry and the Doctor have been rejected despite expressed interest and her one attempt with someone she didn't know well ended very badly. Chakotay was really her only option left at the time.
Chakotay's later-season distrust for Seven of Nine, and dangerous stations in general, could have been caused by Seska's betrayal in earlier seasons.
Why was Voyager designed with manual door releases that can go offline, a holodeck that has a different incompatible power source and gel-packs that easily can get infections and are impossible to replicate? This is indirectly the fault of Geordi LaForge. Why? Because he was mentioned in TNG as having a competition over better warp core efficiency with chief engineer Kaplan of the Intrepid, the prototype of the same class as Voyager. Because Geordi kept trying to beat him in their warp-core output, Kaplan likely got so obsessed with building the Warp 9.975 core to beat Enterprise's Warp 9.8 core, that he either didn't pay proper attention to the other systems or intentionally padded his results. This definitely would explain why Voyager seems to be so slap-dash and haphazardly built.
Concerning the episode "Good Shepherd:" It seems odd at first, that these three crewmen have gone five years without their performance problems being noticed. But, all three of these crewmen were from Janeway's original Starfleet crew. Over the first two years in the Delta Quadrant, Voyager has been dealing with violent and insubordinate Maquis crewman, and just when that problem began to calm down, Voyager gained Seven of Nine. No wonder Celes, Billy, and Mortimer's performances weren't noticed for so long; they may have had trouble with their work, but they didn't have the outrageous attitude problems that so many of their shipmates did!
Given how Mortimer Harren has a job that he does by himself, deep in the bowels of the ship, far away from the rest of those idiots with whom he's been lumbered on a ship for some 70 years, of course he'd never have any big problem with any of his colleagues. He never sees them!
Seven of Nine's voice used to grate on me. Generally people lacking emotion or speaking dispassionately can still inflect normally. Data and Spock did. But it's not the actress doing a bad Spock impersonation, it's the character, in her attempt to deny her emotions.
This troper has wondered to himself why Seven of Nine is so damn hot. Then it hit him, Seven has had her biological functions (particularly hormonal responses) manipulated and largely suppressed so as to avoid cybernetic rejection (a common problem with real life implants) Most likely The Doctor pumped her full of drugs to reactivate her hormonal development in some way, likely including estrogen and goodness knows what else, of course her body went sex-pot.
Actually, if you want an explanation for Seven's... "physical perfection", it does make a lot of sense. When she was assimilated by the Borg she was 6 years old. Then she spent 5 years in a maturation chamber where she was aged artificially. Any physical imperfections or structural asymmetry would have been restructured and enhanced with Borg cybernetics. The Borg are obsessed with perfection. It makes sense that when they mature their drones, they would enhance all physical attributes to maximize physiological potential. In other words every time the Borg mature a drone from childhood, behind their cybernetics they are all altered to exhibit the most perfected aspects of their genetic phenotypes (species inclusive).
Seven's catsuit and heels were likely chosen by Seven herself. The catsuit is "efficient" for mobility, and devoid of what Seven would no doubt deem "irrelevant decorative elements." As for the heels, she probably picked them so she wouldn't feel short and inferior to anyone else board.
In "Parallax", Seska tells Chakotay, "We heard a rumor" that the Maquis crew-members would be confined to quarters, after Torres struck Carrey. We never learn where this absurd rumor came from, but it's plausible that Seska herself started it, as a way to manipulate the Maquis into taking the ship.
At the end of the "Year of Hell" two-parter, Janeway smashes Voyager into the Krenim time ship and presses the reset button (how very original for the show). Voyager is fine and go on their merry way, nobody remembers anything from the past two episodes. And the villain is seen spending time with his wife, whose loss had been his motivation. But if everything had been reset and nobody remembers anything, how is it that the events didn't just repeat themselves? Because everybody remembers unconsciously and their behavior is altered somewhat to prevent the events from occurring. If not everyone, at least the Krenim who built and flew the ship. Otherwise, with their Empire fully restored, there is no reason why they wouldn't build their timeship again.
In a very circular way there is a reason why: it's already happened. Due to the nature of time travel, when Voyager presses the re-set button it's after the Krenim built their timeship. And hence it is always after the timeship is built that Voyager destroys it.
His primary motivation to build the timeship was to restore the Krenim empire, in so doing he caused his wife to be erased. He and his crew were at it for two hundred years was he could never restore the Imperium and his wife. The reason events can't just repeated themselves is the Timeship was erased from history it was never built because he spent time with his wife rather then finish the research.
In "The Cloud", Janeway and Chakotay are discussing animal guides and Janeway seems enthusiastic about the idea, going so far as to go through the whole ritual to contact her animal guide, despite being a firm believer in science and the scientific method. But this is still relatively soon after they were pulled into the Delta Quadrant. The Starfleet and Maquis crew are still adjusting to working together. This is Janeway's way of bonding with Chakotay, by become personally invested in his spiritual beliefs.
"Coda" certainly demonstrated that she hadn't just forsaken all rationality, but "Sacred Ground" also demonstrated that Janeway's logic could be flexible enough to leave some room for supernatural and other trans-rational interventions even as she usually continued to pursue rational and scientific explanations for the majority of anomalies she and her crew experienced.
The end of "Course: Oblivion" frustrates some fans, who wish that the duplicate Kim had been able to tell their story to Voyager before dying. But Voyager, the Enterprise (both of them), and the Defiant run across destroyed ships all the time, dead crews who'd been together for years, who never got to share their stories. Now we know how those crews feel.
"Pathfinder." So, Voyager has had several adventures in which they went through hell and back again, trying to get home or at least make contact with Starfleet, only to fail. Then, one day, when absolutely nothing is happening, they suddenly get a message from Starfleet, out of the blue. That irony is nothing short of brilliant.
The episode "The Fight" explains a hell of a lot about Chakotay's personality. He's able to stay calm and professional despite his strange shipmates and the bizarre situations they get into, because he's punching out all of his adrenaline on the holodeck. (presumably, he got his adrenaline out in battles when in the Maquis.) He's also been playing the Only Sane Man since childhood, when he was expected to watch over his mentally ill grandfather. Up until this episode, Chakotay never much flinched during a battle or in a life threatening situation, but became quite jumpy when something began to mess with his mind (as seen with his fear of assimilation in "Unity"; his reaction to not knowing if he's asleep or awake in "Waking Moments"; and his reaction to the Borg in general). This is because Chakotay's not afraid of physical injuries... only mental ones. In "Memorial" he is far more controlled when his mind is being tampered with, taking the lead when Harry, Tom and Neelix lose it; this is about a year after Chakotay overcame his fears in "The Fight," and he's had a year to meditate on it. He is still angered when he learns that someone deliberately built a mind-altering device, and wants to have it destroyed.
The reason Seven starts acting the way she does in "The Voyager Conspiracy"? She just artificially induced schizophrenia in herself. One of the theories about schizophrenia is that a person's brain starts seeking and making patterns that don't exist. By dumping too much more information into her brain than it could handle in such a time, she induced it to start making connections that didn't exist.
There is also another aspect that validates this theory. One particular facet of schizophrenia is paranoia and deriving connections and patterns from external sensory information that has been interpreted and extrapolated in an irrational manner based on subconscious fears. She has now been given a new load of external data and starts interpreting that data (data which is so densely integrated that meaningless connections exist anyway) based on a paranoid elaboration of her fears. And what does she fear most?
Paris using the holodeck to make a working movie theatre. Torres points out the apparent ridiculousness of this, seeing as how you can just have the computer make the imagery three dimensional. However, if you are watching a movie, more than half of the scene is off camera; if you made the movie three dimensional, you would have to recreate those parts of the scene or it'll look terrible. The story would either have to be adapted to your physical presence or else treat you as an intangible and invisible observer to ensure you couldn't derail it. You could design the other half of the scene yourself, but that would take a lot of work and probably wouldn't look right unless you are a veritable genius at adaptation and interior decoration. After all, a lot of movies are shot on sets and these sets are usually only half of a room. Ironically, making the scene more life-like and three dimensional would tend to destroy your Willing Suspension of Disbelief and prevent you from immersing yourself in the story.
Actually what Belanna considered ridiculous was making a 3d movie theater to play 2d movies that ineffectually simulate 3D. Tom replicated a theaters worth of red/blue 3D glasses for gods sake.
Species 8472 are almost built on Fridge Brilliance. In the episode "In The Flesh" Janeway and the Voyager crew are able to negotiate peace with species 8472. And this has been regarded skeptically by fans considering that species 8472 were always Scary Dogmatic Aliens who want to purge the entire galaxy. Voyager and the audience have always been shown that these aliens were a greater threat than the Borg because of their desire to purge all other forms of life and their advanced technology to do so. They even made telepathic contact with Kes informing her as much. However, when you think about it, the fact that Janeway and her crew were able to make peace makes a lot of sense. Species 8472 lived in fluidic space completely alone, with no other life forms and nothing to threaten or harm them. Then suddenly their universe is invaded by a ship from another universe with other life forms aboard. And not only new life forms but the Borg! If that was your first contact with a form of life that you'd never even conceived of before, you'd probably react similarly. They are absolutely terrified by the Borg and they have no idea that any other forms of life exist in this new universe. Why would they? They were the only ones in their universe so they probably figured the Borg were the only ones in theirs, or even that if there are other life forms they are all violent and destructive like the Borg - and they have no evidence at all to the contrary - (this is already corroborated by what we find out from "In the Flesh": that really all Species 8472 are absolutely terrified of this new violent universe they've found). So when they drive the Borg out of their universe, they are panicked by this new and frightening discovery, and they decide that the Borg are far too dangerous to just drive into retreat - what if they came with a new invasion force or a weapon of mass destruction? - so they go out into the Borg's universe to destroy them (and any other forms of what they presume are violent life) i.e. they want to "purge" this universe, and are pretty determined to do so. With all this fear driving them they present a menacing telepathic presence as well, like they did with Kes in "Scorpion", trying to drive away these new frightening life forms by making themselves as scary as possible. (Considering that they are the only forms of life in fluidic space they have never come across microorganisms either, so when they come into our universe and find bacterial, viral and parasitic diseases everywhere, they probably thought a bacterial disease was another form of invasion as well, or at least an insidious biological threat - this explains why they associate humans with disease, considering humans are completely riddled with micro-organisms). After a violent and bloody war they finally do find out that other life forms exist (and maybe they find out that they aren't all violent), but are worried about humans helping the Borg. They research about the Federation, but all they've seen of humans is humans helping the destructive life forms trying to invade their universe. So finally when Janeway sits down with them and talks it out, they start to understand what is happening and lower their guard, finding out that their fears are unnecessary. Although Species 8472 are first seen as Scary Dogmatic Aliens they are really a terrified race of highly advanced beings who are discovering an insanely alien universe that makes no sense to them and has threatening aspects to it. Once they get used to things they are probably very reasonable, nice people who would make a very good ally for the Federation.
In the finale, "Endgame", Admiral Janeway is able to contaminate the Borg Queen with a pathogen that kills her, and disrupts the entire Collective. This piece of Applied Phlebotinum seems to come out of nowhere, more so because she actually gets it from her younger self, Captain Janeway. Why has Captain Janeway never used this super-weapon before if she had it? But then one realizes that the younger Janeway has had the pathogen since "Collective". It is the Brunali pathogen that Icheb was genetically-engineered to produce. The pathogen was of limited use against the Borg for the Brunali because the cube Icheb was assimilated by never came into contract with any other Borg before succumbing to the pathogen. Likewise, Janeway always knew that she would only have a limited chance to use the pathogen since if she somehow spread it too widely in the Collective eventually they would adapt and become immune. But the older Admiral Janeway's possession of a vehicle that could get close to the Borg Queen at the Primary Unicomplex led to the pathogen infecting the one piece of the Collective that truly connected to everything else, the Queen herself. Especially since the Queen just had to go ahead and assimilate Admiral Janeway personally.
If you pay close attention to the wedding scene in the prologue of "Course: Oblivion", Paris was still referred to as a Lieutenant. This is the first subtle Foreshadowing that something isn't right, since he was demoted to Ensign earlier on in the season, and will not be reinstated until two season later.
Kes' photographic memory makes sense when you consider that she's a member of a species that only typically lives about 10 years. It's possible that an endemic memory is an adaption that the species evolved to get the most out of the few years available, and they would have much less useless junk in their heads than a human would as a result of their shorter lifespans as well. It would be a good explanation as to why Kes is only 2 years old yet somehow manages to not be the same way we are at the same age.
Considering that Neelix has consistently lied about his abilities, and has gotten people killed because of his supposed "skills", it's unlikely that Neelix would have a happy afterlife at all. Being stuck in oblivion is punishment for those wrongful deaths... unless the Talaxian Gods felt a better punishment was forcing him to be sent back to Voyager.
As SF Debris pointed out, Voyager records the crews brain waves all the time.
Fridge Brilliance (again): It's probably the transporter that does this, and considering all the times that a transporter record has saved the day, it's not inconceivable that the records would be stored for a while.
While it's Played for Laughs for us, the war between Dr. Chaotica and the photonic beings in "Bride of Chaotica!" was surely no laughing matter to them: that's a real and fully sentient person the fictional Chaotica casually murdered with his ray gun in one scene! Considering that the victim certainly had good friends and may well have had a family who'd be bitterly grieved and angry to hear about his death, the violent response of these aliens to Chaotica's cruelty is thoroughly justified. Captain Janeway should be grateful the photonic beings never really did figure out what was actually happening, as this first contact would have been a complete diplomatic fiasco for the Voyager and the Federation if they had.
According to Neelix, his grandfather was Myleean, a species with a fused spinal column that prevents them from humanoid locomotion. While they were happily married according to him, the fact we are also told that the Talaxians were once warlike implies that they may have conquered this world, where the peoplecan barely walk!
Considering how "Non Sequitur" shows that even talking to a former Maquis can get a person strapped with an tracking bracelet by Starfleet, do you really think that they are going to exonerate a former group of terrorists?
The episode "Before and After" is LOADED with Fridge Horror.
Kes and Tom's daughter Linnis, and Linnis and Harry's son Andrew, were defined individuals with personalities and histories... and once we got to know them, they were erased from the timeline. On the other hand, if that timeline hadn't been erased, Miral Paris would never have been born, Seven of Nine would never have been freed from the Collective, Janeway would be dead, and everything B'Elanna had been through from Season 3 onward wouldn't have happened to her. The really creepy part? All of these things are true because of one stupid mistake the Doctor made, when he designed the Stasis Chamber to extend Kes' lifespan. His one mistake changed who got to continue living, and who got to be born.
Season 6 Episode Episode 23 "Fury", we learn that after leaving Voyager Kes became a bitter, old woman who felt that she wasted her life on her Voyager to the point where she wanted to go back in time and destroy Voyager and herself. Keep in mind, she didn't want to go back in time and prevent herself from being on Voyager, she was so bitter and angry because of what a pile of crap her life became she wanted to DESTROY Voyager, Janeway and herself out of revenge. They stop her, and she decides to return to her home planet and live out the last few dreary years of her wasted lonely life on her home planet. Okay. Then you remember Season 3 Episode 21 "Before and After". In this episode, in the future, we see Kes is an old woman on board Voyager near the end of her natural 9-year lifespan, dying of natural causes, the natural cycle of life of her people. She is suffering from Ocampa Alzheimers, but she is surrounded by her husband Tom Paris, her grandson, and her daughter who is married to Harry Kim. Though she is suffering from dementia we see that she lived a happy life on Voyager, had a good marriage, raised a happy family, was surrounded by friends and has helped Voyager get that much closer to Earth. She was accepting of her death because she lived a good life and is now going to pass on as people do. So, in an effort to extend her life unnaturally by AT BEST one year where upon she would then die anyway the Doctor tries a radical new therapy that results in her going back in time... and PREVENTING this future from happening, and resulting in her crapsack future. In an effort to prevent her natural life cycle in exchange for at best one miserable dementia ridden year, the Doctor totally wrecked the rest of Kes' entire life, dooming her to live in lonely, miserable anger and waste her life. Nice going, Doc.
Another for "Before and After:" Linnis Paris fought against the Doctor's attempts to extend Kes' life. Linnis thought she was only fighting for her mother's well-being. She had no clue that she was really fighting—and losing—the battle for her own existence, and that of her son Andrew. On the flip side, her losing that fight was the tiny thing that saved B'Elanna Torres, Miral Pairs, Kathryn Janeway, Seven of Nine, the four Borg children, and the millions who Voyager saved in "Endgame" after crippling the Collective.
In "Fury", we never know exactly what happened to make Kes so pissed off during her time away from Voyager. While she claims that the Ocampa rejected her when she returned, it's possible that she was lying. Since this is five years later, this is exactly the same time that the Ocampa would have run out of the power given to them by the Caretaker, meaning that's entirely possible that the Kazon managed to breach the forcefield and enslave them. Or even worse, when the Borg allied with Voyager during "Scorpion", they somehow learned of the Ocampa and their potential for very powerful psychic abilities.
Actually that's a misquote, she said they might reject her. No doubt meaning she'd been too afraid even to approach them.
It was also Canon Discontinuity because she had supposedly become an Energy Being and Ascended to a Higher Plane of Existence. She was also powerful enough to hurl Voyager thousands of light years closer to the Alpha Quadrant. Then she comes back as a God in Human Form, with great, but greatly reduced, powers. She is a physical being again, has aged and is using a ship to travel through space. No explanation for why she reverted to mortal form was given. Even stranger, if she really stopped to think about it, her people would be in desperate need of her powers and protection, since the energy the Caretaker left them would have been pretty much gone. So her evolved state, whatever it was, would have been a blessing, not a problem.
Ascended: In Season 4's "Demon", the crew finds puddles of goo that become sentient and copy the entire crew, complete with memories and the desire to go home. It wasn't until Season 5 ("Course: Oblivion") that the terrible implications of this were addressed.
"Equinox" ends with Janeway accepting the surviving Equinox crew-members onto her ship, but punishing them, by reducing them all to the rank of crewmen. Crewmen. CREWMEN. On a "STAR TREK" ship. And after this episode, we never saw any of them again. Janeway's been the star of a "Trek" series for five years at this point; she knows perfectly well what the rank of "crewmen" does to a person's odds of survival on a "Star Trek" series. It was a stealthy, unofficial form of execution.
Seska stealing Chakotay's "DNA" while he was unconscious. It's obvious that by "DNA" she means "sperm." Exactly how she got his sperm into her body... there are a few possible ways, each more disturbing than the last.
She used a collection device similar to how cows are milked.
She jerked him off.
She stabbed him in the nut with a syringe needle.
She straight-up raped him. And then Seska had the gal to tell the Kazon that Chakotay had raped her.
The fates of most of the senior officers, had Voyager not gotten lost in the Delta Quadrant...
Chakotay, B'Elanna, Chell, Ayala, and the other Maquis would likely be killed by the Dominion or imprisoned by Starfleet-assuming they didn't get killed in the Badlands.
Seven, Icheb, Mezoti, and the twins would still be Borg drones.
Tom and B'Elanna's would never have met, and their daughter would never have been born.
The Doctor would still be a mindless appliance (or at least treated like one), slaving in the mines with the other EMH-Mark 1s.
The characters have brushes with death on a regular basis. But even so, just a few get honorary mention, for Fridge Horror...
In "Caretaker," if Janeway had allowed Tom Paris to be the pilot from the start, rather than an observer, he would have been at the helm instead of Stadi, when Voyager was pulled into the Delta Quadrant. Meaning Tom would have died instantly, as Stadi did.
"Scorpion:" If Seven of Nine hadn't been at the right place at the right time, where she could grab onto something and hold on long enough, without getting sucked into space with the other drones...
Mentioned above, under the "Before and After" section. If the Doc hadn't made one tiny mistake, Kes's future would have remained. Which might be lovely for Kes, but certainly not for B'Elanna, Janeway, Miral, Seven of Nine, Icheb, the Borg kids, and arguably Chakotay (who'd have lost his best friend), and Tom (who'd have lost B'Elanna).
To expand on the above, given how often Seven would go onto save the ship, they'd all be dead if she had gotten spaced in "Scorpion". Even if they'd managed to solve the various crises themselves and even managed to build the Quantum Slipstream drive without her assistance, without Seven's cranial implants to send a message back through time in "Timeless", the entire crew save Harry and Chakotay would likely have been consigned to spend eternity trapped inside an icy glacier.
When the show announced that Ocampa only go into estrus once in their lives, fans started asking how the species managed population growth.
The Ocampa were a dying species who had not only lost the bulk of their telepathic abilities but their lifespans had regressed so far they die at around nine years old. They DON'T manage population growth as they're dying out because they don't live long enough for multiple fertile cycles.
However, they also said they've lived there for 500 generations. To be left with at least one person by the end of that, and accepting that each generation would be half as big as the previous, they would have to have started with something like 2^500 people (about 10^150). For comparison, there are only about 10^80 atoms in the known universe.
Combine what we've been told, and a more plausible explanation emerges, along with a bit of Fridge Horror: the female Caretaker's Ocampa had about twice the lifespan Kes and her people did, and were much better at using their telepathic abilities; they were indicated to be returning to their species' former vigor. It could well be that a lot of those 500 generations were longer-lived than the current one and did have more than one reproductive cycle and therefore could sustain their numbers. By the time Voyager arrived, however, the Caretaker for Kes and her people realized their lifespans and reproductive capacity had degenerated alarmingly, was unable to reverse the process, and was trying to hold out a little longer so as to make their extinction less painful. His last-ditch effort to build up their life support reserves before he died was because he thought if he could send them enough, it would last them for the remainder of their generations, which by then were steadily dwindling by half.
Chakotay also talks about the standard Native American "A man does not own land." This is despite him becoming a terrorist to defend his land.
To defend land that somebody else decided they owned, people already living there be damned.
Even though not all groups of First Nation tribes and empires had that philosophy about land and the Federation offered everyone on those planets a new home.
That's still forced relocation.
It wouldn't be the first time. In the TNG episode "The Ensigns of Command" the plot of the week is that there is an undiscovered human colony on a planet that the Federation had ceded to the Sheliak more than a century earlier. Data had to be somewhat aggressive in illustrating why the colonists needed to leave (because the Sheliak were going to kill them). It was openly-stated that neither the Federation nor the Cardassians were happy about the exact planets they had to exchange to avert further war. This parallels many cases in Earth history outside of North America (most especially in Europe) where war-ending treaties left dissatisfied people in the uncomfortable situation of having to relocate or else find themselves under the sovereignty of a different government.
Star Trek has always been (correctly) vague about the exact velocities of warp drive, to allow Traveling at the Speed of Plot. But in this series Tom Paris mentions that Warp 9.9 means going about 4 billion miles/sec. Light itself only goes 186,000 miles/sec. The Hand Wave is that Voyager can only sprint at 9.9 for very brief periods of time... because, if that speed was sustainable, they would have gotten home in 3.2 years.
To its credit, that Hand Wave has been with the franchise pretty much from the start: whenever the plot demanded it, Kirk could always tell Scotty to give the Enterprise an extra-hard push over its top speed, but it was always for some emergency, and of course Scotty always got to complain that "she cannae take much more o' this, Captain!" The Voyager presumably had a higher top speed, but the same general idea applies: Torres can't push the speed up over warp factor 9 for very long, or she'll blow the warp engines. Moreover, unlike Scotty, she's generally not exaggerating when she assesses Voyager's vulnerabilities or how long repairs will take if Janeway pushes the ship too hard.
The Doctor's Heroic BSOD after choosing to save his friend over someone he barely knew could have been resolved in a much simpler manner: by assigning a higher priority to a member of the ship's senior staff than to a below-decks nobody.
Which would doom Kes, Seven and Neelix to lowest priority as they're not actually members of Starfleet, same would go for most of the former Maquis crew.
A bigger question is why an emergency hologram wouldn't be equipped to handle this sort of decision. An emergency hologram that can't perform triage? What good is that?
This was addressed in the episode: the problem wasn't that he couldn't make the choice logically (by choosing the Bridge officer over the below-decks nobody). It was that he instead allowed his personal bias to make the choice for him, and he saved Harry because Harry was his friend. He went into a feedback loop over the situation because he acted emotionally instead of logically, and his system wasn't able to process the guilt that he felt from it.
If the doctor is in fact a program being run by the ships computer and his physical form is merely a construct of the holo-emitters in the sick-bay, why can't the emitters in the sickbay project multiple doctor-forms that are able to perform tasks on multiple persons at once? Or better yet just use the holo-emitters to directly manipulate physical objects in the room as necesssary and when possible simulate equipment that need to be duplicated, (I never understood why Kes needed to be around to hand objects to the doctor; a hologram manipulating physical objects in a room is just another way of saying the computer is performing telekinesis). Presumably the computer processing power required to run the Doctor isn't so great that it would destroy the ship to temporarily shunt some extra processing power to the sickbay to run procedures at once during an emergency?
The reason is stated that the Doctor's program is a highly complex system and rather power intensive. Trying to run more than one of him would be difficult given the constraints of the sickbay, since he was originally only meant to be a temporary measure at most. This was addressed in the episode with the Cardassian consultant program, where with only a fraction of the complexity of the Doctor's program, it still repeatedly suffered from glitches and system crashes. In short, the Doctor is simply too complex to duplicate and generating more of him is feasible, but really difficult and you'd more than likely end up having his dopplegangers vanishing in the middle of performing delicate surgery.
By the beginning of Voyager, they already know that there's a stable wormhole in the Gamma Quadrant that would take them home; it's almost guaranteed to be closer to Voyager's location in the Delta Quadrant than a straight line drawn to Earth would be and at this point they've never heard of the Dominion. Yet the possibility of making a bee-line for this potential shortcut is never raised
It wouldn't be any closer and they'd still have to cross a large portion of the Delta Quadrant just to get to the equally unexplored Gamma Quadrant. And by that point they were vaguely aware of the Dominion so they knew there was a hostile force waiting for them in the Gamma Quadrant.
There is no way to know the exact locations between Voyager, Earth, and the Gamma Quadrant end of the Bajoran Wormhole. It's possible that it could be even farther from Voyager than Earth. Granted they could have just thrown it away in a few lines ("Could we head for the Bajoran Wormhole instead?" "No, it's actually farther away from us than Earth, and there's no way to know if it'll still be stable by the time we get there." "Oh, okay.")
In point of fact - Voyager launched from DS9 after the incident with the Dominion mounting a suicide run against the Galaxy-class U.S.S. Odyssey as of Star Trek: Deep Space Nine season 2 finale - they had to have known about the dangers of the Dominion in the area.
Basically all the times when the Department of Temporal Investigations don't show up when there's time travel causes a great deal of Fridge Logic. They do, after all, have time machines, it's not as if they can't find Voyager. After having been introduced, they're conspicuously absent from the two occasions when Voyager is saved by people deliberately breaking the Temporal Prime Directive in order to alter the past and, ironically, the only time they actually do show up it's to solve problems which they themselves are the cause of. The only explanation - not just for this but for why they don't pop up all over the franchise - seems to be that they're willing to turn a blind eye to anything that benefits the Federation
Actually, it makes perfect sense, once you think about it - the Department of Temporal Investigations is itself subject to the Temporal Prime Directive. Any time travel that occurred exclusively prior to the formation of the Department would not be in any way subject to alteration by them, as that would itself change the future, possibly screwing with their own timeline. While Voyager's regular temporal mechanical complications are difficult for the DTI to keep track of, they're also entirely built into the DTI's timeline, especially given that some things that led to the formation of the DTI were likely inspired by discoveries made by Voyager and events triggered by Voyager. Indeed, the big question is why the DTI don't consider Voyager to be kind of an essential part of their history, and thus worthy of real fascination (rather than simple frustration).
The Expanded Universe novels suggest that the organization was created by events much earlier than the era of Voyager and they never went easy on other ships and captains. It seems more likely that either the writers simply forgot that the organization existed or that the organization hadn't been thought up in DS9 at the time the Voyager episodes were being written.
It's possible that the majority of time travel Voyager was involved in was always meant to happen so they just ignore those cases. Stable time loops were even mentioned in the episode Seven and Janeway worked with them.
In "Scorpion" I and II, we get our first glimpse of Species 8472's home, "Fluidic Space", a Lovecraftian realm where there are no stars, no galaxies, no planets near as we can tell. Everything is suspended in liquidious green goo. Soo...isn't "Fluidic Space" a contradiction of terms? The whole place is filled with fluid, i.e. matter, i.e. not vacuum, i.e. not space. "Fluidic Universe" would've flown fine, but then that'd make sense...
B'Elanna actually makes this observation in the episode:
Torres: The entire region is filled with some kind of organic fluid... this isn't space... it's matter.