(Disclaimer in advance : I still love this show & very much liked this episode. Just not this part: )

Totally fair. I'm probably going to argue a bit against what you say here, but I appreciate that these are thoughtful critiques and not just haterade.
M'Benga's secret is exactly as "dark" as Una's:
It's not their own fault, they're actually good people yada yada, and in oldTrek none of these would be an issue as the Federation would help with their resources.
Well, I suppose I would indeed argue that neither M'Benga's nor Una's secrets are dark. I would consider them
dramatic secrets but not dark.
And I don't know that the Federation in oldTrek would have helped with M'Benga's child by essentially "freezing" her in a transporter. We've never heard of anyone from the TNG or TOS era essentially freezing a loved one with a terminal illness long-term, whether in a transporter or in cryogenic freeze or stasis. McCoy didn't freeze his dad, for instance.
I'm sure there are Federation scientists trying to cure her disease back on UFP worlds.
But at the same time - they absolutely lied to get on board, Una must have had faked a shit-ton of medical examinations, the doctor sneaked a freakin' child in a box on board & told nobody that turning the power of will kill her and both basically put other people's trust and life at risk.
I believe the implication is that nobody else's life is at risk, only Rukiya's.
In nuTrek the Federation is always dumb, prejudicial, and it comes down to the strong man defying stupid regulations. That's too easy.
I don't agree with that assessment. There have definitely been times when the Federation did dumb or prejudicial stuff, but there have also been plenty of times it hasn't. It was Michael whose prejudice helped ignite the Federation-Klingon War in S1, for instance; Federation principles might have avoided conflict if Michael hadn't attacked the Torchbearer. It was Section 31 that unleashed Control and almost got everyone killed in S2, and it was Starfleet proper that saved everyone. Pike may have violated General Order 1 by revealing himself to the Kyleans, but he preserved the intent of the order by refusing to intervene any further than telling the Kyleans what had happened to Earth in WW3, and his actions in "Children of the Comet" were framed as the Federation's will rather than defiance of the UFP's will. The Federation is absolutely framed as doing the right thing most of the time in DIS S3 and S4 -- the Federation's rejection of Emerald Chain greed is vindicated, and its rejection of aggression and embrace of diplomacy towards Species 10-C is depicted as absolutely the right thing in S4.
Honestly I don't think modern ST depicts the Federation as a power structure as being in the wrong any more often than TNG, DS9, or VOY did back in the day.
Also, not EVERY freakin' character needs a dramatic backstory! It's allowed to just have professionals on board doing an interesting but dangerous job.
I just can't relate to this criticism. I would generally err on the side of characters with interesting backstories than ones without. But so far, Ortegas, Chapel, and Hemmer all just seem like professionals doing their jobs -- no dramatic backstories as far as we can see.
Yes. But it messes with the whole "Federation discriminates against outsiders"-thing this episode was going for. They're clearly on good terms with Denobulans from ENT to LD.
Yeah, that's part of why I interpret the Illyrians as Humans. To me it makes more sense that Earthers would feel entitled to discriminate and "other" the Illyrians if they're a nation of Humans who left Earth to practice genetic augmentation than if they're aliens.
And sorry for being harsh - but sneaking a child on board that can accidentally be killed by someone else pushing the wrong button, and then endangering the whole crew to protect that secret, makes him utterly unfit to work on a starship & he should be released from duty. (But Starfleet scientists should still working with him to find a cure back on earth).
Well, we know from TOS that by the 2268, he's serving aboard the
Enterprise again but he's no longer CMO. So that strongly implies to me that he's going to face some sort of accountability for his decision to smuggle Rukiya aboard but that the punishment won't include expulsion or imprisonment. Which I think sounds reasonable, and speaks to the Federation as a more just organization in modern ST than you were arguing.
But still. Not a good look. And especially not a good introduction to the character.
Oh, I liked it! I can relate to a guy willing to break a large bureaucracy's rules more than I can to a company man.
The consistency of Klingon and Romulan appearance, then.
Totally fair point! Like I said, it's completely legitimate to interpret the SNW Illyrians as the same species as the ENT Illyrians. I don't share that interpretation but it's totally legit.