Darren Mooney: Henry Archer only got to Warp 4 and only served a single term as President of the Cochrane Institute. Jonathan showed him.
In Season 3, he is embroiled in war against Xindi and their WMDs!
Due to Archer's inconsistent behavior in the first three seasons, SF Debris loves to riff that he's actually an insane homeless man Starfleet found living in a box somewhere. Given some of his orders during the show's run, Chuck's theory actually might not be too far off.
This all depends on another Alternative Character Interpretation: were the Vulcans mildly restrictive guardians of Earth trying to keep a lid on a violent irrational species clamoring for advanced technology and privileges when they weren't ready, wanting to protect humans from the Galaxy and the Galaxy from them? Or were the Vulcans overly restrictive interlopers who betrayed their own Prime Directive on non-interference and interfered heavily in a paternalistic manner, giving them their protocols for basic deep space exploration but giving them almost no information on different species, their politics, boundaries, advanced diplomatic techniques, and other information that would be vital for interspecies relations because they didn't want to encourage the humans to go beyond simple meet-and-greet diplomacy... so when Archer and his crew blunder into an interspecies situation, they have almost no idea what to do, what to expect, or how they should act.
The numerous actions by Phlox that go against all medical ethics caused a theory that when the Federation was formed, the Denobulans weren't included due to their abhorrent ethical standards, hence why this prequel series is the first we've ever heard of them.
“One day, Starfleet will draft a Directive...that is Prime!… A... “Prime” directive, if you will…”'' Bakula deserved an Emmy for getting through the speech straight-faced.
The season 3 episode Chosen Realm. Plenty of religious extremism, religion used to justify suicide bombings and other killings, etc. It also doesn't help that the ending is a quite shameless ripoff of the famous Some Anvils Need to Be Dropped Original Series episode "Let That Be Your Last Battlefield."
"Carpenter Street" feels like an early Star Trek: The Next Generation episode, as it takes every opportunity to lecture its 21st century audience about how backward their society is. Fossil fuel, smoking, and fast food are all ridiculed.
Otherwise, despite the Issue Drift, season 3 managed to avert this trope (narrowly) with regards to the Xindi main storyline.
Ass Pull: Quite a few episodes involve aspects of the Trek universe from a century or two in the future, with horribly nonsensical contrivances to avoid actually messing with canon. Most noticeable is the Borg not identifying themselves for no reason at all except the Enterprise-D crew didn't know who they were at first.
The Vulcans in Enterprise (particularly T'Pol) were criticized by viewers for acting very un-Vulcan-like, nearly indistinguishable from Romulans. This was used as the basis of a three-episode story in the fourth season involving the Syrannites, an orthodox sect of Vulcans (in contrast to Vulcan society which has "strayed from Surak's teachings"), and the discovery of the Kir'Shara (the original copy of Surak's writings). It is said that Season 5 would have tried to explain why T'Pol is more emotional than most Vulcans by revealing she was actually half-Romulan.
Another complaint was how the show did nothing to show the formation of the Federation. Again, this was addressed in the fourth season with a three-episode story that showed the beginnings of alliance between Humans, Vulcans, Andorians and Tellarites (the Federation's four founding species) as well as the formation of the "Coalition of Planets" in the penultimate two-part story.
Also, the greatest one of all, "Judgment", which turns the entire Klingon race from a gigantic flanderization to a retroactive Tear Jerker that shows that the warrior caste took over the Klingons' entire culture slowly over several hundred years. By the time of Star Trek: Voyager, the warriors are all that's left.
Basically, Season 4 can be seen as one really long Author's Saving Throw... because they got a new head writer, who promptly set the writers' team to cleaning up the mess of his predecessors. It wasn't perfect, but there was reasonably only so much they could do in one season, as well as devoting so much time to retconning the three previous clunky seasons.
Although re-hashing the "Augments" issue in such a predictable way after the massive attention it got in DS9 was an example of the writers of season 4 having some of the same issues that previous season writers had.
Base-Breaking Character: Let's just say the misguided argument for withholding a cure from the Valakians in "Dear Doctor" is just one reason Phlox is Star Trek's most divisive doctor.
Kathryn Janeway was controversial, but not quite like Jonathan Archer. He gets accusations of Designated Hero more often than any other Trek captain, for his bitterness toward the Vulcans, amongst other things, leading him to some reckless decision-making (for example, he's as culpable for the result of "Dear Doctor" as Phlox, and he's also come under fire for his decisions in "The Andorian Incident" and "Cogenitor"). They made his greying morality a more central part of his character during the Xindi arc, resulting in a more interesting character, though that hasn't done much to fix the base-breaking.
Best Known for the Fanservice: Enterprise has a bit of a reputation for being more 'adult' than Trek series before, with a bit more bad language slipping through and edgier characterization. Oh, and extra Fanservice - T'Pol is not-so-subtly an Expy of Seven Of Nine, complete with a Stripperiffic outfit, and then there's the infamous decontamination room, an excuse to get everyone down to their underpants Once an Episode.
Better on DVD: Very much a Love It Or Hate It show on its original run for both its concept and also because it was the last piece of Star Trek to be made in an unbroken 18 year run on TV, ingloriously cancelled before it reached the expected 7 seasons; the advent of the franchise's revival in the JJ Abrams directed movies, coinciding with the release of Enterprise on Blu-Ray, has resulted in a sizable shift in appreciation from some quarters of the fanbase. It's not uncommon these days to hear it being spoken about as an under-appreciated gem.
Well, Season 4 to be sure, and mostly Season 3. The first two are still pretty much treated the same.
In "Broken Bow", after Archer gets shot in the leg, he has a flashback to his childhood recalling some advice his father gave, then he suddenly sees T'Pol standing there glaring at him. The scene was so jarring that it generated heaps of Epileptic Trees that devolved into nothing when there was never any further reference to it.
The couple of times in the first season when the crew are having casual conversations while rubbing each other down with gel half-naked in the decon chamber. It came completely out of nowhere. The only possible reason why one of the scenes occurred was because it featured T'Pol and Trip rubbing each other down while arguing, which could have been foreshadowing for their relationship developments in season 3, but even that explanation is reaching.
The Star Trek fanbase in general is divided up between people who think Enterprise was either an ambitious-if-flawed series and those who think it was deservedly cancelled. The split likely occurred during DS9/VOY's run. Those who craved realism and space politics had their own show with DS9, while the TOS lovers had their seven years of VOY (If you hadn't kept up with DS9 or VOY, "Broken Bow" had two or three scenes that old-timers would probably find distasteful). Both sides got funneled into watching ENT. Toss in the TOS fans lured by the promise of classic Trek adventures, and you wind up with an unpleasable hydra.
The Agony Booth:With a lot of old-school Trekkies (understandably) seeing Enterprise as an attempt to 're-do' TOS, and with a lot of new-school Trekkies (understandably) pissed that the new show wasn't going to build upon the TNG-DS9-Voyager continuity, the show went on to polarize fans like never before. If you feel indifferent towards Enterprise, chances are you're not really that into Star Trek.
There is a serious divide among fans of the series over the closing "These are the voyages..." narration in the last episode. Some fans thought it was cool that they divided the narration up among the various Captains of the Enterprise, while others saw it as a Take That! to Scott Bakula, who (they argue) had earned the right to make the entire narration himself.
A similar break was caused by the 2009 reboot when Leonard Nimoy gave the narration rather than Chris Pine. This was fortunately resolved in the sequel.
The Broken Base reached its climax around 2002-2003 when, coupled with the failure of Star Trek: Nemesis at the box office, Trek fandom fractured into "bashers" (those who could no longer abide anything related to Trek made by the then-current production regime) and "gushers" (who generally defended the current works, but were scorned by the bashers for blindly liking whatever was put in front of them). As the first Trek series that lived and died during the Internet age, Trek forums were frequently the site of figurative bloodbaths, with both bashers and gushers being banned for flaming each other. There were also some extreme reports of fans claiming to want to do physical harm to Enterprise's producers, and one forum saw an infamous exchange where a fan claimed to have gotten so upset at the news that the Borg were to appear in Enterprise that he smashed his television. When Enterprise finally did end, many fans divorced themselves from "Trekdom"; the JJ Abrams reboot (which divided the fanbase even more) won some back, but others moved on to other franchises.
The Broken Base effect was further emphasized by the fact that whatever the showrunners tried to do to address concerns was slapped down: fans were upset the series didn't have Star Trek in the title. The title was added, and they were criticized for doing so. The "Temporal Cold War" plotline was abandoned due to being unpopular; they were criticized for abandoning it. An attempt at breaking status quo with the season-long Xindi arc was condemned by the same people who said they wanted Enterprise to stop being a clone of Voyager and TOS. Even the final season's "Hail Mary" pass of devoting most of the season to prequeling TOS and TNG, something fans had wanted since day 1, was rejected. Ironically, the series was officially cancelled during production of an episode that replicated the costumes and sets of the Star Trek TOS era. But by this point the base was so broken that had William Shatner and Leonard Nimoy become regulars the fanbase would have still turned up their nose at it.
To any moderates or anyone with any opinions that fell between the battle lines, this Broken Base could lead to absolute lethality in the forums. God help you if you thought the series was a reasonably enjoyable, if flawed, prequel that despite problems actually did quite well with the material it had to work with, showing an imperfect crew who struggled in defining their place and the place of humanity in a quite often hostile galaxy - making mistakes along the way (probably unintended by the writers but which had greater meaning and ramifications within the context of the show) - with the improvements in season 4 making astounding retroactive sense out of many of the issues of the series and Star Trek franchise. There are a small group who feel that despite the wasted potential of plot lines and canon, and a handful of rather painful episodes that pop up here and there which are drowned in Moral Dissonance, hypocrisy and stupidity - like "Dear Doctor" for one - this was still a rather enjoyable show. Of course, expect to be called a troll if you voiced such an opinion at the time. You could get slaughtered (bloodily) in the forums from both sides for voicing any of this interpretation, particularly if you never payed any attention to any Word of God information given about the series, and ended up thinking that the series fitted in with continuity, or, horror of horrors, that the Temporal Cold War was an interesting mostly background arc that gave maneuverability and flexibility with regards to whether the series would end up leading into the franchise continuity or into an alternate timeline, giving a more dynamic appeal to a series that could otherwise have been boxed-in by franchise canon.
On the other hand, there are some fans (especially those critical of the reboot) who dismiss any criticism of the show and blame fans for "ruining the franchise" by not supporting the show enough.
The launch of Star Trek: Discovery has caused yet another fracturing of the base, with some claiming that Discovery has helped them gain a new appreciation of Enterprise, for at least trying to stay true to the spirit of Star Trek even if the execution wasn't always that great, and just as many claiming that Discovery shows up how outdated Enterprise seemed even when it first aired (and that's before you get to those fans who love both shows, or don't like either of them).
The Chris Carter Effect: Many fans doubted whether the Temporal Cold War arc would ever make sense. To some fans it never did, although this might have been a product of the nature of the storyline more than anything else. The perspective on the Temporal Cold War was from a point in time when the ramifications of time travel and time travel laws meant nothing, and despite a lot of the action in the Temporal Cold War occurring during the 22nd century, the after effects and temporal-ramifications could never be made clear unless someone from the future with access to a view on the timeline showed it to the protagonists or explained it to them (an exposition that would frankly have made no sense considering the Temporal Prime Directive), since we only saw the War from the protagonists' perspective. The audience only got a look at a snapshot in time, and considering the limited perspective, it was only ever going to be the case that we saw the battles and not the war. However, considering the fact that Enterprise did occur in continuity with the other series (in the end anyway), you can deduce - taking into account information given about the 29th century during the series - that those on the side of the Temporal Accord won anyway and history turned out fairly well (although how much deviation and damage occurred to the original timeline (whatever that was) is unknown). To most fans the biggest problem with the Temporal Cold War was its wasted potential (see below), and the awesome opportunities for temporal anarchy that could have been exploited but weren't.
Complete Monster: Season 3's Xindi Arc is already dark, but Commander Dolim stands out as one of the darkest villains on the show. Dolim was the leader of the Reptilian faction of the Xindi civilization. When interdimensional aliens known as the Sphere Builders want to conquer the future by making sure The Federation never exists, they lie to Xindi, telling them that humans will destroy their civilization in the future. The Xindi launch an attack on Earth, which causes the deaths of 7 million humans. While most of the Xindi leaders express regret over what they have done, but see it as a Necessary Evil to save their civilization, Dolim revels in the fact that he helped to kill so many humans, gloating to Archer that he personally selected the pilot of the probe that attacked Earth. When Archer presents evidence that the Sphere Builders are lying, many of the reasonable Xindi leaders are convinced, but Dolim will not even consider the evidence. Dolim kills Degra, the Xindi primate scientist who designed the sphere probe, for helping Archer and promises to hunt down Degra's family after he has destroyed the Earth. Dolim also uses torture to get cooperation from Archer and Hoshi. Dolim loses any pretense of noble intentions when the Sphere Builders convince Dolim to continue with the mission to destroy Earth, promising him they will make the Reptilians rulers of a new Xindi Empire if he succeeds. The Reptilians and Insectoids hijack the Sphere probe, with the intention of using it to wipe out all life on Earth. When his Insectoid allies begin to question this mission, Dolim has their ship destroyed without a second thought, believing they were no longer necessary.
Contested Sequel: See above. Not even Voyager spawns quite as much bile as this show does, and debates about the merits of every element continue to this very day.
Epileptic Trees: A theory that existed as far back as the pilot episode was that Enterprise was actually a Show Within a Show in the world of TNG-era Trek, which explained the more advanced-looking technology and supposed continuity errors. This remained a fringe theory in Enterprise fandom for several years, until the series finale was shown to have a holonovel of the Enterprise as a framing device, and all of a sudden the theory was taken a lot more seriously.
A nice addendum to the theory would be that with the Xindi incident and the Earth-Romulan War, most of the missions relating to the NX-01 were heavily classified by Starfleet, which remained in effect even into the 24th century, out of fear that some of Enterprise's more dubious activities might have damaged the Federation if word ever got out. As such, Enterprise is merely the revisionist history known to the public.
In "Dear Doctor", Archer and Phlox decide not to give the Valakians and Menk a cure to their illness, likely dooming both races to extinction, and this decision helps Phlox gain new respect for Archer? This can be blamed on Executive Meddling; the episode was supposed to end with Archer and Phlox at odds with each other (Archer wanting the cure, Phlox opposing it), but the network didn't want any disagreements between them. So what should have ended up as a debate on the morality of intervention on the fate of another species with heavy consequences, turns into everyone deciding unequivocally that of course it's right to doom millions to die based on some warped Darwinistic ideal of naturalist succession.
"Bound". The idea behind it was noble, but it did it in a half-baked manner. Offering a clichéd appropriation of third-wave feminism suggesting that the Orion Slave Girls are “empowered” by their sexuality and are the ones calling the shots. (The sex slaver is a brain-dead zombie... Didn't we already do this story in "Angel One"?) Which feels like an excuse to justify the cheesecake scenes and lingering male gaze that runs through the episode.
Trivia: Star Trek had a deleted scene where Kirk mixes up another Orion with Galia, which seems like the film calling Kirk out on treating alien space babes as interchangeable.
Bakula himself suggested Archer's middle name is Beckett. OHBOYYYYYYYYY...
The Denobulans have never been seen in any other Trek series. An interpretation you'll come across sometimes is traced to Phlox and his, let's say, questionable decisions over the course of the series, such as the numerous times he breaks doctor-patient confidentiality, and the infamous "Dear Doctor." Once the Federation began and the Blue and Orange Morality of Denobulan medical ethics came to light, perhaps one side or the other realized that the Denobulans are probably not a good fit for the Federation.
A large portion of the fanbase rejects the series finale "These Are The Voyages". Some of the actors have publicly and vocally done so as well. Some people reject it entirely, while others reject it as a historical fabrication thanks to the fact that it took place on the Enterprise-D's holodeck. The Expanded Universe novels take this latter route.
Darren Mooney: This puts Enterprise in the rather strange position where three of its final five episodes do not feature any of the primary cast, instead focusing on doppelgangers or holograms. Perhaps this is a reflection on the show’s attitude towards its place within the canon. Perhaps Enterprise fears that it will be a secret history, a forgotten story populated by spectres and echoes.
The funny thing is that there is no ''need' to reject the finale. The finale is a holodeck recreation and so is by nature an interpretation of what happened and an Unreliable Narrator. It suggests what may have happened and the circumstances but beyond that it could easily have been wrong because of misinformation or Starfleet classifying certain facts. There is no possible way you can say that what was shown in the finale was what actually happened unless other evidence was shown in the TNG-era corroborating it. You can take the finale as is and still have it make perfect sense with the Expanded Universe novels.
Quite a few fans rejected "Bound" for pushing the boundaries of consent of the male crew, on top of the heteronormativity.
A vocal contingent of fans reject the entire premise of this series, saying it violates canon by its mere existence. Of course, most of the supposed canon violations (such as Starfleet already existing, a Vulcan serving on a starship, Klingons already having brow ridges) aren't really canon violations at all, and while the use of the name Enterprise for a famous pre-Federation ship is problematic and confusing, nothing from the other series conclusively proves the Enterprise NX-01 never existed. Some take the above-mentioned "These Are the Voyages" series finale as an indication that the entire thing was just "Riker playing on the holodeck", which is of course ridiculous.
"Funny Aneurysm" Moment: In "Dear Doctor", Dr. Phlox and Crewman Cutler have a discussion about the heart's place as the emotional center for humans, which ends with Cutler saying "you may know about our cardiopulmonary system, but you have a lot to learn about the human heart.". Cutler's actress, Kellie Waymire, would die from a heart defect in 2003.
Season 3 or 4. Both seasons (particularly the latter) were far and away better received than what came before.
This actually ends up being Fridge Brilliance because what we see is the Enterprise crew having a rocky start, getting involved in dubious incidents and making mistakes and judgement errors, and then they grow steadily more competent and are shown getting involved in important matters and making wise, experienced decisions. In an in-series manner, the show Growing the Beard reflects on the characters and what they do, which actually shows Character Development. Especially in Archer, who, after the events of "The Expanse" at the end of season 2, gradually turns from his naive "aw shucks" demeanor, to a much grittier, determined approach. Sadly, none of this was quite enough to overcome the loss in viewership and fandom goodwill.
A lot of fans point to season 2's "Cogenitor" as ENT's first genuinely excellent episode; at the very least, it's one of the show's most controversial.
Harsher in Hindsight: In many ways, Season Two's "Regeneration" is a quintessential "in-universe" example. Part of the thrill of the episode is the fact that viewers with even a passing familiarity with the Borg are far more aware of what the characters are up against than the characters are... and thus, the fact that they're all in grave danger.
In a first season episode, someone is amazed at how far Archer and his crew have come, and asks him what things have been named after him back on Earth. Archer laughs this idea off, but it's revealed later that, eventually, two planets were named after him.
For those who feel that Archer's skills as a "trained diplomat" are an Informed Ability, the scene in "Broken Bow" with the Klingon High Council, where Hoshi basically tells Archer that he doesn't want to know what the Chancellor said to them, the TNG episode "First Contact" becomes especially hilarious:
Picard: Centuries ago, disastrous contact with the Klingon Empire led to decades of war.
After the show's cancellation, fans attempted a campaign to fund a fifth season. Disregarding a substantial donation made by a group of people in the aeronautical industry, it only raised a little over $100,000 (enough to produce about a tenth of one episode), and was widely seen as a dismal failure and proof that the remaining Trek fans were at best overly dedicated to a franchise that was increasingly irrelevant, and at worst flat-out delusional. Fast-forward to the modern day however, and various types of media (including a continuation of Veronica Mars, the show which UPN canned Enterprise to focus their resources on) getting funding through Kickstarter, it appears that the campaign to save Enteprise was actually way ahead of its time, and just lacked the infrastructure to succeed.
Not precisely hindsight, but if you've ever seen Casablanca, the "Storm Front" episodes—Humphrey Bogart was right when he told Colonel Strasser that "there are parts of New York I'd advise you not to try and invade."
"Terra Nova" could have easily been resolved long before the episode, had Earth simply asked the Vulcans to investigate, or if they had simply ignored the mere 200 or so colonists' objection to any more people landing on the same planet (planets are big, after all).
The Kreetassans' Hat is that they have extremely strict decency guidelines and have zero tolerance for anyone who breaks them. Except, they've clearly been out in the stars and interacting with other races for quite a while, so you'd have to imagine they've realized by now their own cultural practices are very much in the minority and they should warn any new contacts about them.
Iron Woobie/Stoic Woobie: Reed. Really, the guy should be given a medal for the number of times he's been shot, concussed, crushed under rocks, pinned to the hull of the ship by a Romulan mine, almost hanged, etc.
A major complaint about Enterprise, particularly the first couple seasons was how strongly similar it was to all the previous Trek shows, particularly Voyager. It took the threat of cancellation to make them do something with the premise.
To the point where even though the technology won't be invented in the Federation for another two centuries, the fifth episode featured an alien holodeck, while the eighth episode has the replic- sorry, Protein Resequencer, capable of turning human faeces into a pair of boots. "Protein synthesisers" look more than little like food replicators. (Kirk had to get his sandwiches from a vending machine.)
More damagingly, Rick Berman had been the man in charge of the franchise since Gene Roddenberry's death, and in the first two seasons fans got the distinct impression that his mindset was still stuck in how television worked at that time, ignoring how the format had been revolutionized starting in the late '90s to feature heavy serialization and few standalone stories. However, when the series did adopt this format (season 3's Xindi arc; season 4's mini-arcs), it was rejected (and indeed, even today there is serious discontinuity in various fandoms between those who want serials and those who prefer standalones. See Doctor Who.)
As a rule, Bakula is not an actor whose style lends itself to big sweeping speeches and grandstanding. But the show seems to spend a significant portion of the first two seasons hoping that he can pull it off like Shatner and Stewart.
The whole "Vulcans don't believe in time travel" thing, which was derided by many fans as a hackneyed attempt to make them look bad so the humans would look better in comparison, and making less and less sense as the show went on with T'Pol putting Agent Scully to shame with her refusal to believe the increasing mountain of evidence.
The infamous "A Night In Sickbay," amongst other things, gives us Archer having a nightmare about going to Porthos' funeral, which segues into a sexy dream about T'Pol. It's supposed to be titillating, and thanks to the Mood Whiplash, it fails miserably.
Narm Charm: "It's been a looooong road... gettin' from there to heeeere..." Somewhere between a Creed ballad and Air Supply, the Enterprise theme is both mocked and remembered fondly in equal measure to this day.
Never Live It Down: Phlox, and by extension writer Brannon Braga, advocating genocide in "Dear Doctor" through the exact same misunderstanding of evolution that the Voyager episode "Threshold" is so infamous for.
Nightmare Fuel: Tarquin in "The Exile." Someone from a planet many light-years away who invades Hoshi's thoughts, reads your entire past and all her current thoughts with total accuracy, and makes contact with her in a way that makes her think she's going crazy, hijacks her senses so she hallucinates him on all the viewscreens in the room (which you know, isn't a scene out of the horror genre or anything), and then tries to coerce her into staying with him forever by faking that Archer is going to abandon her there. (And then he attacks her ship.) Want to make stalking even scarier than it already is? Give them long-range telepathy.
Berman and Braga. Of course, it doesn't help that in addition to writing some of the more notorious and critically panned episodes, they penned the much-loathed finale and believed it to be "a Valentine's to the fans". At first, anyway. Both Berman and Braga would later admit that they regretted the finale and understood the backlash, with Braga apologising for the latter comment on the Enterprise Season 2 Blu-Ray, believing that this was rather a narcissistic statement on his and Berman's part.
The Scrappy: "Future Guy", due to being a major part of the loathed Temporal Cold War storyline and such a poorly conceived character, to the point that his true identity was never revealed. Especially embarrassing as he was meant to be the show's Big Bad.
Shocking Swerve: The ending of Season 3. After a season's worth of fighting Xindi, talking to Xindi, and being informed by Daniels that the Temporal Cold War hinges on correctly resolving the Xindi situation, the crew finally stops the Xindi weapon and gets ready for a heroic homecoming only to find... Nazis have taken over the world. Because of the Temporal Cold War. Not only did this completely pull the rug out from under the dramatic finale episodes, it came with no foreshadowing whatsoever and had nothing at all to do with the Xindi.
Snark Bait: As the final installment in an unbroken 18-year run of Star Trek television shows, Enterprise was perhaps doomed to this status no matter what, but the generally low or inconsistent quality of the writing, lack of memorable or likable characters in contrast to most Star Trek crews, the highly confusing Temporal Cold War plotline, an overreliance on what had come before, and a widely despised final episode have perhaps cemented the show's reputation forever as "that show after Voyager that almost killed the franchise."
Some Anvils Need to Be Dropped: Although Pa'nar Syndrome is seen as Anvilicious, at the time this series was made the issues brought up and points made about this illness with its likeness to AIDS was necessary. Even now the issues brought up are still true, vital to be reminded of and thought of, and remain so for other illnesses as well.
Squick: When Trip and Hoshi get all sweaty when they have a silicon virus. Especially when Hoshi throws up.
In Fortunate Son we're obviously supposed to disagree with the humans on the freighter who are trying to attack a base of Nausicaan pirates because the humans tortured a prisoner for information and the man in charge, Matthew Ryan, is clearly obsessed. However Ryan has a point. So far Starfleet and the Vulcans haven't done a single thing to stop the pirate attacks and the freighters have to endure constant attacks by far stronger pirates. The episode itself seems to unconsciously admit this when Archer can't think up a good counter to Ryan's complaints.
Archer in "The Hatchery." He decides they have to keep it running; when the crew protests, Archer says it's the same as if they'd found a nursery full of humanoid babies and saving the hatchery could serve as a point of truce between them and the Xindi, relating a story where soldiers in the Eugenics War called a truce so they could move the battle lines away from a school. Pretty in-line with Star Trek's themes of respecting life even in forms we're unfamiliar with, right? NOPE. This is irrational behavior that leads to Archer genuinely jeopardizing the mission and T'Pol has to mutiny against him. The only reason Archer wants to save the babies (weird, alienbug babies, guys!) is because he got some egg gunk on him that made him reverse-imprint. Once Phlox fixes it, he's perfectly happy to ditch the hatchery with the Hand Wave that "they'll survive until a Xindi ship finds them."
Could go for many characters, but Travis Mayweather in particular stands out. Born and raised on a space freighter, he had the most practical space experience of the entire crew, despite his relative youth and low rank in Starfleet. The writers never seemed to grasp the inherent hooks of this, however, and the poor ensign had more or less nothing significant to do during the show's entire run (That is patently false! In the series finale he got a name tag). Indeed, this even led to an unintentional subplot in the second series, where it seems that every other episode Travis was injured and sent to sickbay, simply to give him a reason to appear in the episode. It's also become a popular speculation that after "Fortunate Son" was intended to be Travis's first big focus episode, the crew was so disappointed by Anthony Montgomery's performance that they decided not to ever give him such a large role again.
Hoshi Sato being reduced from bridge officer with a vital role and Archer's old friend... to the ship's unofficial errand girl and glorified intern. This was an unfortunate side effect of the retool the series went through after its first two seasons. Those first seasons put more emphasis on exploration, first contact, and establishing peaceful relations between humans and various other species, all of which gave Hoshi a lot to do. But the third season was one big war arc, and the fourth had a lot of emphasis on armed conflict too, so the role of the ship's communication officer was understandably diminished.
The Mirror Universe versions of Hoshi and Travis taking over the Terran Empire at the end of that arc can only be a nod to their underuse in the prime universe.
Malcolm Reed, who served in freaking Section 31 before joining the Enterprise crew. For the unaware, this is the branch of Starfleet that is roughly on par with MI-6 in terms of undercover operations. In other words, James Bond was the weapons officer of this ship, and he wasn't even a part of the Power Trio! Malcolm's Section 31 past was retcon added to the character in the middle of Enterprise's final season, so it's not like they had much time to develop this element before the show was cancelled.
To a lesser degree, perhaps one of the few interesting characters in "Broken Bow" was Sarin, the Suliban Cabal defector who is killed after only a few minutes of screen time. One could imagine that she could have made for a great recurring character and foil to Silik, as well as emphasising the threat of the Temporal Cold War dividing entire races into factions, especially if could happen to Humanity as well.
Emory Erickson from "Daedalus", the inventor of the transporter, first human to be transported and like a second father to Archer when he was growing up. The episode could have been far more powerful and tragic if it was revealed he was simply hallucinating his son Quinn being trapped mid-beam, a delusion caused by Transporter Psychosis that was common during this time period due to the imperfect technology. Likewise it would be tragic for Archer, being forced to watch yet another father-figure slowly lose his grip on reality.
Most fans believe that Berman and Braga wasted a perfectly good show.
During the finale, there's a subplot about the epic speech that Archer gives that will go down in the history books. Don't expect to see it.
It probably isn't an exaggeration to say that most fans expected to see the groundwork being laid for the future series; specifically the Romulan war and the leadup thereunto, as well as the infancy of the United Federation of Planets. There was the odd first encounter with an established race, but this happened incredibly infrequently, and usually didn't lead to much in the way of development. It didn't help that Brannon Braga apparently only set the series that far in the past so that he could get the franchise back to what he thought was its roots: the idea of deep space exploration. According to him, Star Trek was meant to be about exploration but the latest Trek series had gotten away from that.
Which, ironically, is exactly what they missed out on actually doing. In TOS, the major canon races (Klingons, Romulans, etc.) were introduced without any prior history beyond exposition given in the episodes in which they appeared. Audiences were meant to "recognize" them more based on the fact that they were expies of America's rivals in the Cold War, not because there were piles of canon and EU material about them. ENT could have actually put more time into developing the discovery of species that would play a major role in later series. Instead they devoted that effort to developing races that were mysteriously absent from the other series, such as the Suliban and the Xindi.
The entire Temporal Cold War idea was completely wasted. This idea had a huge amount of potential. There could have been crossovers with the TNG, DS9 and Voyager crews in order to save the timeline, going back to help ancient humans, explaining myths and legends from Earth itself and different cultures. In fact, they could have even gone forward in time to show the infancy of the federation, if the show creators didn't want to put that in the 22nd century! They could have explained a lot of species backstory and laid down huge swaths of canon without even having to put it into the show timeframe. An insane amount of good ideas were just sitting there inherent in the introduction. Even the Suliban could have been made into a great plot. And all of it gone to waste, and in such a way that fans were practically begging for the Time War plot to end because it was so irritating. We never even found out who the Suliban's future sponsor, the guy originally set up as the series' Big Bad, really was... but the Temporal Cold War had gotten so boring by the time it was ditched that few cared anymore.
SF Debris went even further with this, saying the conclusion to the story could have been Archer's crew solving everything at the cost of being erased from the timeline themselves, creating a very moving story about heroes no one would ever know about, and also neatly explaining why such apparently massively important historical figures had never been mentioned in the franchise until now.
On a smaller scale, imagine how neat it could have been if Daniels had been a minor character throughout the first half of season one, occasionally showing up just to deliver news and such, before revealing he was a Time Agent? Instead, the reveal falls completely flat when we've never heard of him before the episode.
Also, the Temporal Cold War itself wasted the initial premise of the show. Enterprise was supposedly a prequel exploring how humanity took its first steps into the stars, leading to the founding of the United Federation of Planets and Starfleet as we know them. . . and the Temporal Cold War means you're not getting a show about that, you're getting a show about some jerks from the future trying to screw with that.
On a variation, there are a lot of episodes early in season 3 which were completely unnecessary. The Xindi plotline was - despite the Issue Drift - really rather good, and the episodes which dealt explicitly with it were engaging and interesting. But there were a good fifteen or so episodes that could have been used to flesh out the Xindi and the Sphere-Users. Instead we have things like humans being abducted from the Old West and the crew finding an almost exact recreation on an alien planet where they were prejudiced against aliens instead of Native Americans. Yeah, what stunning and original racial commentary.
In regards to the above "North Star", it's even more bizarre that Mayweather doesn't appear in that episode, nor do we see any black characters on the planet? You'd think that the scenes where the natives defend their belief that Aliens Are Bastards for enslaving humans, only to be shot down when it's pointed out that at the time of their abduction (the 1860's), humans also practiced slavery against other humans?! Furthermore, are there other ethnicities on the planet and if so, are they still prejudiced against them as well? The scenes practically write themselves, yet these things are never addressed?!
The Enterprise XCV-330, the early Starfleet vessel with a ringed warp drive is never shown, despite being alluded to in the design of the Vulcan starships, which evidently inspired the human engineers to build their own version. "These Are The Voyages" similarly wasted a good opportunity to show the Daedalus-class as being the new Warp 7 vessel replacing the NX-series, since TNG revealed the class was in operation during the 2160's.
Taking place before it existed would have been a perfect chance for Deconstruction of the Prime Directive and the moral hazard of its more dogmatic interpretations, perhaps with a realization of becoming Not So Different from the obstructionist and racist Vulcans. Instead we got things like “Dear Doctor”.
Unintentional Period Piece: Several elements clearly identify the show as belonging to the early Aughts. The cast includes two main characters who bear strong resemblance to George W. Bush. The subtly named antagonists of the first two seasons are the "Suliban". The third season's Xindi arc is launched with what is essentially space 9/11. Parodied by The Onionhere.
We're Still Relevant, Dammit!: The series never quite recovered from the shock of 9/11 in its first two seasons. (Which is a callous thing to say about a tragedy like that; its effects on the Star Trek franchise aren’t near the top of anybody’s concerns, obviously, but bear with us.) Several cast and crew members knew people who died in the attack. The third season works quite well as a metaphor for Star Trek trying to work through that shock and trauma, beginning in a very cynical and dark place, but ending in a more utopian mindset.
Duras waits until Enterprise reaches the Solar System until he attacks, allowing Starfleet to quickly deploy reinforcements and drive him off.
The Xindi attack Earth with the prototype superweapon for no apparent reason. They didn't have any way to predict Future Guy cheating and telling Archer about them, but if they hadn't attacked at all, there never would have been any search for the weapon and Earth would have been destroyed.
How about the fact that Starfleet didn't seem to mobilize its Solar System Defense Forces until after the weapon was destroyed! The twenty or so ships we saw welcoming Enterprise back would have been helpful against the Xindi weapon and the ONE ship escorting it!
Alternate!Archer from "E2" had over a century to meet with the Xindi, offer them aid, and rebuild their civilization (Xindis had only just been destroyed), and gain their eternal gratitude. Instead, he pisses the opportunity of a lifetime away, ordering them to fly around the Delphic Expanse. It's not like he cared about trying not to change the timeline either! Several crew members are from races he went on to make contact with whilst in the past, including the woman who would become his wife! But hey, it's not like anyone died as a result of your sitting on your hands, right? How are Tucker's sister and those 7 million people, again?
WTH, Casting Agency?: Bakula is one of the sweetest and most charming actors working. But Star Trek has a very firm and rigid idea of what a commanding officer should be ( "Ours not to wonder why, ours but to do and to die!") The points where Archer comes closest to working as a character are the points where he seems like a less-stereotypical Trek captain.
WTH, Costuming Department?: The bowl-cut that T'Pol sports is frequently derided by fans, particularly since female Vulcans seen in the TOS-era had a variety of hairstyles, making longer hair hardly canon-breaking. And her wardrobe in general. (We can see Jolene Blalock is a beautiful woman; you don't need to paint on her catsuits to prove it, or make her change multiple times an episode.)
Many fans have also cited her longer hair in "Twilight", "E2" and "In A Mirror Darkly" as being a vast improvement, wondering why it has to take a Bad Future and Alternate Reality for her to get a decent hairstyle?
Tucker often falls into this. Tucker's clone Sim from "Similitude" even more so, being created solely for organ harvesting for the injured Trip and living just under a week.
Hoshi Sato. No doubt, there's a damn good reason Archer needs her out there, but between her claustrophobia and general awkwardness - not to mention the abuse she takes through the series, especially "Countdown" - she's clearly bitten off more than she can chew with this position, and gives off a bit of a Shrinking Violet vibe. Starts to overcome this at the end of the series (unfortunately by then, she'd gone considerably Out of Focus).