"Mirror, Mirror" gives a pretty good picture. And imagine all of Star Trek: Voyager with the evil crew from "Living Witness."
Alternate-Archer from the Mirror Universe, over the course of the episode begins to experience vivid hallucinations and demonstrates progressively more erratic behaviour that according to Forrest was previously atypical from him. Did he suffer a psychotic break, or is he beginning to display several of the symptoms of Clarke's Syndrome, the illness that killed his regular-universe counterpart's father? If so, what does that bode for his counterpart?
Keep in mind, Arik Soong postulated a possible cure could exist and the Denobulans could have researched one, given how they aren't against genetic engineering like Starfleet. It is possible that in our universe, Archer could have developed the condition and been treated for it.
When one looks at the evidence, the Xyrillians from "Unexpected" look very suspiciously like date-rapists. First, they stalk Enterprise remaining in their wake to avoid detection, only to claim their ship is broken down when caught. Any visitors experience a Mushroom Samba due to their unique atmosphere, forcing them to take a nap for the better part of a day or two. In Tucker's case, he's shown the wonders of the holodeck and invited to play a game, which is actually their form of sex, essentially subjecting him to rape! (Which she later reveals she knew what she was doing). When their ship is finally fixed, they seem to be in quite a hurry to depart, only to run into the same mysterious "engine problems" a few days later when they're found trailing behind the Klingon's ship. Sound suspicious yet? How about the following line;
"We have a lot of experience dealing with alien visitors..."
In "Doctor's Orders", Phlox is forced to remain awake while the rest of the crew are put into a coma to travel through a dangerous region of space. The problem however is that unlike the episode it's recycling, "One" from Voyager, Seven lasted about three weeks before the isolation started causing her to hallucinate, before finally going off the deep end when the Doctor went offline. In this case of "Doctor's Orders" however, Phlox is only alone for four days and cracks up after two of them. Furthermore, it's stated that this hallucinations under extreme stress is considered normal for his species and is not a side effect of the region of space they are travelling through! In other words, this unintentionally paints the picture that Phlox's mental health is constantly teetering on the precipice of full-blown madness!
Bearing in mind that "In a Mirror Darkly" shows us the mirror versions of Phlox and Reed are the agony booth's inventors, and that the first prototype of the booth was later destroyed along with the Enterprise, one of its inventors has to have survived; by Kirk's time, the agony booth had been propagated to all Terran vessels. Since Phlox was most likely executed for his attempt to sabotage the Defiant (and most certainly would not have given his executioners any help in making his execution more slow and painful than it was already likely to be), Reed, whom Phlox indicated stood an equal chance of dying or recovering after his near-fatal encounter with Slar the Gorn's booby trap, probably did ultimately recover.
Many fans were irritated by the show's treatment of the Vulcans, which more or less made them a whole race of jerkasses. It does, however, give some interesting context to Dr. McCoy's occasionally. . .uh. . .uncomfortable comments to Spock.
Are we really supposed to believe that the Humans willingly let the Vulcans stagnate their technological development for over 100 years? Granted they were desperate for allies and the Vulcans are (mostly) benevolent, but what exactly stopped Humanity from simply trading for a more advanced Warp Drives from another race? Does this mean that the Vulcans confiscated the vessels of anyone who tried? Surely this would have caused Humanity to tell them to go screw themselves and cut off all ties?
Enterprise appears to suggest that before the the Enterprise expedition, humanity's knowledge of what is out there is quite... limited, to say the least (even the Tellarites, who appear to be one of the local relative Great Powers, are unfamiliar to the non-T'Pol Enterprise crew as of season 2). Before you trade for a more advanced warp drive, you need to find someone willing (and able) to sell you a more advanced warp drive, after all.
That being said, we know that Humanity's reach was at least 90 lights years prior to 2151, with Draylax and Vega Colony being some of the furthest locations explored, even before the Warp 2 Barrier was broken in 2143 note Merryweather was born on the several months long freight-run between those two places in 2126. Furthermore, we know that Humanity was in contact with both the Draylaxians and the Denobulans before the launch of Enterprise and possibly a few other races. Unless they all were still limited to Warp 1 and 2, it seems strange that there wasn't at least one enterprising alien businessman willing to flog human explorers a better engine?
But what would humanity have to trade with? Seriously, we're a backwater hick planet with crappy everything. We probably had nothing worth the trader's time.
While Earth is still a backwater, it appears quite wealthy and prosperous as of 2151, enough to end world hunger, disease and poverty. The Earth Cargo Service runs freight to various worlds, so clearly it's not like Earth doesn't have stuff other races aren't interested in? We even see Archer trade supplies for a bunch of kitchen spices in one episode! Taking two ships and selling one, even if for scrap metal and spare parts would earn more than enough for some better kit. Even the Ferengi figured this out and they were too stupid to invent warp themselves!
Most likely political/economic threats from the Vulcans. The Vulcans are shown to be an important player in the Alpha Quadrant, so much so that the Klingons are willing to not send a squadron of warbirds to raze Earth after speaking with them. They most likely exerted their influence to prevent other races from trading with Earth, something along the lines of "If you sell the humans technology that we say they can't have, we'll boycott/blockade your world," or, even worse in cases like the Andorians who the Vulcans don't have amicable relations with, the threat of a shooting war should they interfere. And the Humans, lacking in technology as they were, would be incapable of telling the Vulcans off. "You want us to leave? That's cute. Now, about this warp engine you want to build..."
I was all ready to post a thing on Headscratchers about the Vulcans using lirpas in the Forge rather than the Vulcan equivalent to assault rifles. I figured that as the properties of the Forge are known, they should at least have the Vulcan equivalent of park rangers trained in and armed with these weapons. But then I thought about it, and I realized a few things:
1. Given the significance of the Forge to the Vulcans, the Vulcan priests might well control the Forge rangers. To them, assault rifles or similar weapons would be emblematic of their pre-Surak days, and they would find them repugnant.
2. Even if they did have assault rifles, the Vulcan High Command would not trust these rangers to capture Archer, T'Pol, and T'Pau. If they saw them carrying the Kir'Shara, they might switch sides. And none of their own troops would have reason to be trained to use such weapons. Instead, the High Command found a few trustworthy soldiers who were experts at the ancient Vulcan martial art of lirpa-fu, and sent them in.
Wasn't it mentioned however, that unique properties of the Forge causes interference with particle weapons, rendering them useless?
While the writers clearly intended T'Pol's casting to be for fan service it ended up serving a better purpose, reinforcing one of the few themes they had working in the beginning. When Cochrane made first contact with the Vulcans, we who were masters of our realm were now children again and the Vulcans were adults, smarter and wiser about the new world we were about to enter. By Enterprise era, we're in our late adolescence, having grown up faster than our parents expected, chafing under their rules, ready to break out and explore the world on our own. But they were still smarter and wiser. This is all reinforced on the Enterprise with the adolescent acting Archer butting heads with the calm measured presence of T'Pol. She was smarter, more experienced and physically superior; a constant reminder that made the humans aboard feel somewhat inadequate. So it helps that she's also beautiful, which both makes all of that more visually present and makes her seem that much more superior, having seemingly no flaws. This is one instance in which a flawless character can serve the story.
Zefram Cochrane's paraphrasing of the classic introduction from TOS and TNG may seem like a mere Continuity Nod at first. When given a little thought, you realize: Kirk based his speech upon Cochrane's! Picard more likely paraphrased from Kirk, but when you realize that the speech was first made by Cochrane it has much more meaning every time you hear it.
While any fan is loathed to use "These Are the Voyages" as an example, it's subtly implied that the "modern" introduction may have been first paraphrased by Archer. Which means that he was the one most likely responsible for flubbing Cochrane's grammatically correct "let us go boldly", into the more famous version, "to boldly go".
I realize that this almost certainly wasn't the intention, but now that you point that out, I can't help but be reminded that probably the most famous flubbed line in American history also happens to be the most famous (though in no way less inspiring) flubbed line in real-life space exploration:
Neil Armstrong: That's one small step for man, one giant leap for mankind.
Although Armstrong himself always claimed that he said "A Man", but this was lost in the (admittedly bad) transmission.
In "Twilight", why did T'Pol foolishly decide to ram the docked Xindi ship into the other one, wrecking one nacelle and ultimately delay the mission long enough for the Xindi weapon to be launched? It was likely because by this point in the alternate timeline, she was suffering from the effects of Trellium-D, lowering her impulse control. This would also explain the smirk she adopts when she began ramming the ships, she was high at the time!
This could also be the real reason she was selflessly taking it upon herself to care for Archer for all those years. Instead of doing it to repay him for saving her from the anomalies, it's because she's trying to atone for inadvertently causing the destruction of Earth, after she let her addiction to Trellium-D take precedence over the mission, causing it to derail completely.
Hoshi running around being something of an errand girl instead of doing her actual job most of time. The thing is, why wouldn't this be the case? While Archer is the captain and has to run the ship, Reed has to maintain the weapon systems and deal with petty security issues, Tucker has to run the entirety of engineering all day long, and so on, What else does Hoshi have to do? Not much really. The reality is the amount of time she's going to spend actually translating and running the communicator is going to be a tiny fraction of what she's going to spend doing basically nothing all day otherwise. Hoshi's pretty much the only one of the main characters who actually has the time to be a gofer, and it allows her to pick up a wide variety of skills besides.