Why the Federation/Starfleet is a totalitarian regime

[Frost Giant]

Once again, I agree, but if Starfleet is going to employ telepaths on their ships, then it is a considered a form of covertness.

Not necessarily. They could simply inform races they encounter up front that there is a telepath on the bridge. In fact, it would be in the Federation's character to do so. I could easily see that written into their first contact protocol. Also, many of the races they encounter are telepathic themselves and some even disdain verbal communication. Having a bridge telepath would com in very handy there. I still don't agree that something along those lines would make Starfleet a malevolent secret police organization like the Psi Corps.

That means that all the training she's had to become a psychologist was for nothing!

Not really. Her actions just show she's an emotionally fragile person herself. Her throwing tantrums was a more serious concern that her "quitting" which was really only a temporary hiatus from whatever it is she does on the ship. If I was Picard I would have started to doubt her emotional stability. But a tantrum doesn't mean she didn't earn a shrink degree at some University somewhere (even if she did cheat with her empathic sense).
"Yes, this just shows how hypocritical Starfleet is! Gene Roddenberry did not want Starfleet to incorporate cloaking devices on their ships because he said they were not sneaks and yet, he incorporates telepaths to get inside the minds of their adversaries!"
There's a big difference between some archaeologists observing from a duck blind and cloaking a warship for strategic purposes.
While there are episodes involving Spock's mindmelds (both voluntary and involuntary) and Troi's "feelings" I don't really see a Psi Corps-like approach that is standard in Starfleet.

languages have already been deciphered and downloaded into their computer memory banks, and develop the stories that showcase trade and commerce a la Dune. Personally, I think it makes for a far more interesting premise.

It could be that is a component of how the UT works, they don't really delve into details. Speaking of which....

Michael Okuda, graphic designer who designed the computer graphics interface for TNG consoles once said he was asked by a fan on how the Heisenberg Compensators worked and he said, "Very well, thank you!"

If the yardstick for scifi is that the tech presented must be proven in detail, that's a pretty high bar to meet. How does the Heisenberg Compensator actually work? How exactly does the Whitestar on Babylon 5 travel faster than light? You said it best, though....

When it comes to most sci-fi shows and movies, you have to suspend disbelief to an extent.

I believe that the team behind TNG did their due diligence arrived at an acceptable extent. More than many competing sci fi franchises. The typical viewer shouldn't need to crack open a physics textbook to follow a sci fi TV show. I agree that the transporter is a dubious, even horrifying proposition and that it is extremely unlikely in real life.
However, there will always be shortcuts around current limitations of technology and physics, the good part about that is it makes some people dream about what might be possible. In some cases, these people are actually motivated to research or invent something. Sci FI and fantasy allow people's minds to exceed their grasp.
As far as what's credible, that's up to the individual viewer and if it sparks debate that's a healthy thing.