That drum hasn't broken yet, eh?
Regardless of the evil lazy writing
(trademark pending) working in universe shows that dilithium is preferred for a variety of reasons. Omega is unstable unless perfectly handled, and would devastate the local space, making warp drive impossible if it goes wrong. As you note, there are some ores required to make new molecules which means it isn't reliable. Same with the spore drive, as well as the potential impact on the living beings in the mycelial network.
Dilithium appears to be the easiest, most reliable, and flexible enough to accommodate many species ship designs. As the old saying goes, if it ain't broke, don't fix it. I believe the saying originated in Russia.
When Omega was neutralized, it didn't really do large amount of damage to subspace. That was the whole point of building the harmonic rezonance chamber - to stabilize and neutralize Omega... effectively controlling it, at which point, a detonantion of Omega molecule becomes a proverbial 'blip' that doesn't really inconvenience anyone.
And besides, by the mid/late 25th century, you'd expect the UFP would have perfected the harmonic resonance chamber technology to such a degree where they would remove any kind of possibility of Omega destroying anything (or at least, reduce the factor to the same level as M/AM - I mean, ANY technology has the potential for massive destruction if misused). And heck, if a SF crew on a starship with limited resources could do that with the help of a former Borg drone, then just think what they could do if they put some effort into studying all that data upon Voy's return.
Heck, give it 25 years of automated R&D in UFP and that would be more than enough time to cover majority if not all possible scenarios that could occur with the substance in question before you start making the thing, and initiate a decade long transition to non dilithium and M/AM power matricies.
My point is that beyond Omega, there have been several examples of Trek species using power sources without non Dilithium and M/AM which worked just fine.
The writers not progressing UFP beyond Dilithium and M/AM on its own is just stupid and lazy writing for the sake of drama and somewhat anti-Trek.
I'm sorry, but for a space faring organisation comprised of THAT many species working together, that kind of scenario wouldn't have occurred.
And how many new technologies did SF encounter where M/AM and dilithium simply weren't going to cut it?
Dilithium is far from easiest, reliable or flexible ... its just more abundant and inroads were made for dilithium mining and M/AM generation at the start (similar to fossil fuels). You don't stick with something 'just because it works'... I mean come on, we had the ability to move to renewables for nearly 100 years now and the only reason we stuck with fossil fuels was because huge businesses were built around it.
In Trek and UFP, change of that magnitude wouldn't be feared or shunned (no Capitalism to worry about for one thing). The way it was presented, it should be embraced, and people could retrain and transition into a new area of technology - much like animal farmers for example instead of continuing the outdated and grueling practice of rearing and slaughtering animals could grow plants instead - but even that's completely unnecessary when you factor in all the technology and science we developed along with automation.
Its not like people have livelihoods to worry about in UFP which are based around dilithium mining and M/AM (and yes, we have seen Trill families engaging in dilithium mining and being pressured to meet increased demands from UFP, but still... that was before VOY returned), and even Stamets was smart enough to know how dirty dilithium mining was back in the 23rd century - it was one of the reasons he developed the Spore drive.
Also, 'danger to mycelieal lifeforms' isn't really a problem. The path to that option was supposedly 'sealed' so there is no danger of ships destroying lifeforms in the network. Otherwise, Discovery wouldn't have been able to continue using the network for its jumps.
And besides, those aren't the only options. VOY brought back multiple technologies back with it, including the fact the UFP was already researching new power sources during TNG era actively.
Like I said, the writers needed a quick and dirty solution for something that would cripple UFP (and most of the galaxy it seems) to create a 'darker setting' so that Disco could 'swoop in and save the day'.
I mean, they could have delayed the show a bit more and come up with something better instead.
