Risa

For the reward of instantaneous travel, I’m sure the Federation could muddle its way through amending a 100 year old law.

Not really. The Federation, humanity most of all, are aggressively against genetic engineering. On top of it the genetic engineering requires one of those specific species of tardigrade. None were found despite Starfleet having a call put out to go looking for it. Only one was found and that was on accident.

The rest of the points don’t seem all that different than the complications we see our heroes regularly encounter exploring the galaxy.

Navigation in the other Trek shows isn't difficult. It's pathetically simple provided you're not going through some weird distortion or nebula that messes with a bunch of shit. Warp also doesn't destroy all known sentient life in the galaxy. Whether the Discovery keeps using it or not is irrelevant. At the time that the Spore Drive was known, it was not feasible to make another attempt at a spore drive. They did not have any of the originating scientists, they did not have required materials, and they were prohibited by their own law.

Janeway has no reason to be miffed given that she sat on an infinite speed drive herself, which had no downside that the doctor wouldn’t have been able to cure after it took them home.

Yep. That always made zero fucking sense to me. It's proven you can be un-salamandered and they have an inorganic being on board who wouldn't be affected. Why the hell don't they just Warp 10 back to the Alpha Quadrant? Or put everyone in stasis while they Warp 10 over? They've done it before. Janeway doesn't get to complain about a spore drive that would have required her to rebuild the nacelles from the ground up when she was sitting on a way home with a solution and didn't bother.

They've temporally shifted the eugenics wars so they're no longer in the 90s but post those wars? Yeah. Genetic experimentation is still insanely illegal and taboo to all living hell.

There are allowances for genetic therapies to treat medical conditions, but this probably falls outside of that realm just a bit.

Discovery also had hologram communication technology that I guess was also a secret? Starfleet went back to flatscreens for everything and didn’t use holograms again until the 24th century.

In "The Undiscovered Country" we see the Klingons are watching the Federation President's discussion with Azetbur using a grainy hologram. If they're able to receive a holographic signal, that implies that the Federation is transmitting one. Hell, even in the TOS episode, "Return of the Archons" when confronted with the holographic projection of Landru, Kirk and Spock recognize it for what it is right away, but the things they remark upon are the fact that there's no visible projectors, and Kirk says it's "Beautiful."

I don't think it's too much of a stretch based on what we've see to say that Starfleet decided that holographic projections were too low fidelity compared to viewscreens.

Hell, it even happens again. As you note, they made another attempt at holographic communication in the 24th century, which we see in DS9 the Defiant is kitted out with the new holo-communicator, allowing a fully realized, high fidelity, holodeck quality real time holographic communication. And where else have we seen it? We never see the Enterprise E use that technology; In "Nemesis" Shinzon is able to broadcast a hologram of himself from the Scimitar to Picard's ready room, but he claims it's through the use of his own holo-emitters. We've never seen it in LDecks, PRO, or PIC, all of which take place after DS9.

So yeah, Starfleet went back to flat screens for everything.

TNG's and VOY's viewscreens are technically holographic, but the effect is applied inconsistently.