I love this stuff. I'll quibble with a few things.

(1) Conspiracies

I totally disagree. I find long-lived conspiracies quite believable, but with the caveat that they must be socially realistic and have plausible operating principles.

First of all, a long-lived complex conspiracy cannot remain totally secret. That's not plausible. Something's going to leak. But it can act and/or distract (disinformation, etc.) so as to limit the damage and exposure brought about by these leaks. Keep in mind that in today's information overload world the information might be out there but if it's not clamoring for attention it will be ignored. When was the last time you Googled the secret initiatory practices of the Order of the Blahblahblah?

But more importantly: people do not engage in long term coordinated complex action without motive, and just "eeeevil!!" or even just profit or power are not sufficient motives to keep people in a coherent "always-cooperate" game theoretic mode with one another for that long. If power and profit are the motive then the group will dissolve through internal strife. Other motives are needed.

A long-lived complex conspiracy therefore rapidly converges with religion or cult. It must have a Doctrine(tm), an initiation process, some form of eschatology either real or metaphysical, etc. If it's a really nasty cult-driven-conspiracy it might employ cult mind control techniques. These as we know from the real world can be devastatingly effective. Whole massive groups of people have been convinced to commit suicide (Jonestown), so why couldn't they be convinced to perpetuate a lasting criminal or "parapolitical" conspiracy even at risk to themselves and their own personal fortune or power?

A plausible Big Bad X-Files Conspiracy therefore must be a cult and is going to look and operate like a cult. It's going to have internal cult jargon and crazy doctrines that will sound shockingly batshit to outsiders but that internally actually serve as belief-and-language-based social signaling. (Galactic emperor Xenu, etc.) If it's a conspiracy that lasts longer than a life span then it must have a doctrine that transcends the personality of its leadership and some mechanism for transfer of kingship. It's going to have totally brainwashed True Believers following manipulative and obsessed upper management for whom the cult is a proxy for their personal ego. It's going to have some process for both initiating new members and purging itself of dissent. The later is going to look like the shame-driven practices you see in manipulative cults in which the dissenter is first shamed and vilified before being banished or killed.

Profit or power are not sufficient motives, but a "carrot and stick" can be a part of cult mind control. Membership may have its benefits if the cult is powerful, rich, or well-connected, and once one has accepted these favors they are a "made man" indebted to the cult. Blackmail can also play a role. Many gangs and mafia groups require members to commit a crime or misdeed in order to join, and revelation of that crime or misdeed can later be dangled as punishment.

Fundamentally a long-lived conspiracy with coherent goals is going to be a cult that operates a lot like the mafia. In fact it's not uncommon for mafia like criminal conspiracies to have racial identity doctrines, honor codes, a romantic image of themselves, and other mythologies that serve at the very least as social glue. Many began with political goals -- the true Mafia were if my memory serves me originally a political resistance. Combine that with some crazy-ass religion or political eschatology and you've got your cigarette smoking man and his compatriots nailed.

I actually take an opposite tack on conspiracies: while I think the woo-woo variety of conspiracy theory is woo, I also think there's a kind of faux-rationalistic over-reaction in skeptic circles that amounts to "coherent group motive denialism." Conspire just means "to act together," and secrecy through flat silence or through distraction is definitely possible within certain realistic bounds. Hell, if nobody wanted to ever be secret we never would have invented encryption!

Finally though -- it is true that nothing remains the same forever. At some point one of two things is going to happen: the conspiracy/cult is going to act in a big way and in so doing both reveal itself and immanentize its eschaton, or it's going to fade away and dissolve into socioeconomic background radiation. If the group is strongly motivated the former is more likely, especially if it feels "the time is nigh" (it has enough power) or conversely if it feels itself losing power and feels forced to act. Sometimes the latter is driven by the leadership's need to maintain internal credibility. If people start doubting then they must escalate. (Some propose that ISIS is now launching international terror for exactly this reason, though they are far from secret. But the same principle applies.)

... and remember that end-justifies-the-mean fanatics can be very very bad, so we're well into plausible villain territory. If the end justifies the mean and the ideology provides a moral 'out', people will do insanely evil stuff... like... I dunno... tell people gas chambers are showers? Open fire on cafes? Force children to drink poison? Only the author's personal depravity is the limit to what they might imagine such a group plausibly doing when the chips are down.

Who knows, maybe that's a big part of the story? What happens when your dismissed-as-wacko conspiracy nut is proven dramatically "as in breaking news" correct? Or maybe your conspiracy theorists' investigations actually prod the group into paranoia-driven action? Such a group is likely more paranoid than the foil hatters that might chase them.

An alternative plot twist I thought up once for the X-Files and that would fit into the emerging 'rational fiction' trope is if Mulder discovered that while (most of) the paranormal stuff wasn't real and the aliens weren't invading... the conspiracy that The Smoking Man belonged to believed alien invasion was nigh and was all the more dangerous as a result. The stuff that did turn out to be real might have a rational (but perhaps still very SF) explanation... and the conspiracy plot revolves around how its existence has inspired insane paranoia among an element of our intelligence apparatus who are utterly convinced it's a sign of impending alien invasion. Think of it as a more elaborate SF-based version of a comet inspiring a dangerous doomsday cult. The big finale could have been Mulder now struggling to find a credible way to reveal the truth about UFOs (which might still have a neat SF edge... von Neumann probes?) to the world not just for truth's sake but to stop the impending global-scale Jonestown meltdown of the conspiracy.

(2) World-controlling corporations

I sort of agree and disagree. A world-controlling corporation is plausible but will have in becoming such a thing become a government. Therefore you have a similar convergence path here as you do with conspiracy -> long lived conspiracy -> cult. Corporation -> mega-powerful totalistic corporation -> nation state.

To become a government requires that the corp evolve new traits like a national mythology, the adoption of governmental function and ritual, and a support base in the general population. The latter is important: for this to happen, someone has to think it's a good idea!

It's not impossible that a corporate entity could undergo such a metamorphosis while retaining some of its original mega-corp DNA. But it would most certainly no longer be a corporation in the traditional sense. It would have some sort of national identity.

The socioeconomic, political, or technological forces that might push a corporation down this road and lead to it emerging as a government/nation might be quite interesting. It's not at all implausible given that Congress has something like a 15% approval rating.

Here's a back story for you: an aggressive Uber-like startup invents an economically plausible win/win way to shrink the exploding wealth disparity in developed nations... maybe something based on an innovation in game theory. But to make it work they need to change a few laws. Fast forward a hundred years and you have a global socialist state presided over by something that is now a government but retains the organizational DNA of an Uber-like growth company. For its brand of game theoretic win/win socialism to keep working it must meet certain numbers, which leads in practice to some kind of nutty/weird Keynesianism. ... and of course dissenters are provably (via game theory) threatening the well being of all.

That's quite plausible and no idiot ball is required.

(3) Space travel

I disagree that routine space travel is implausible, but I do agree that if you do it and have any hard SF aspirations then you must read up on physics and orbital mechanics. You've got to make a genuine attempt to make it physically plausible... unless of course you're going the SF-flavored-fantasy route of Star Wars in which case that's okay too. In that case it's got to at least be in-world consistent and not terribly cliche.

I do agree that MacGuffins like He3 are unlikely. Really interesting original motives for space travel and/or settlement are much better. These could include necessity (Seveneves), politics (escaping global dystopia), religion (or desire to freely practice such in a world where that's forbidden), weird but plausible economics (after two generations of global Japan-style stagnation, the World Central Bank decides a big space economy would make a better stimulus package than WWIII and launches a PR effort to sell it, etc.), a massive discovery that demands a major exploration effort, etc.

One that I've toyed around with is this: that in an almost post-scarcity and incredibly rich society people might do space travel for the same reason they climb Everest or try to break deep sea diving records... to have fun and show off. Implausible today but not implausible in an economy 10X larger or where technology like reusable spacecraft has geometrically reduced cost. Space travel and attempts at space settlement could be a sport. Think a cross between extreme mountaineering and Nascar.