Wouldn't synthetic dilithium crystals pose a similar problem of the Burn like natural ones?
They'd have to have same or similar properties to work, so not exactly the direction I would take... but I would agree that SF/UFP would have been able to create a synthetic form of Dilithium that works just fine long before Dilithium ever runs out.
If there are any "Subspace Components" to the Dilithium crystals, they can figure out how to shield it or work out some sort of passive defense mechanisms that would make them immune to Sukal's Subspace scream that would shatter Dilithium.
I'm more concerned that UFP/SF actually researched their own new power generation technologies and even encountered/scanned advanced forms of power generation (such as the Tetryon reactor and even Thermionic generators from Species 8472 - while the episode in question didn't specifically indicate they shared this tech with SF, the Delta Flyer took extensive scans of the habitat and 7 of 9 was able to identify thermionic generators as a power source - meaning she knew what they were, and most likely had an insight into how they might work - that alone would have spurred some research into the technology and it probably would have allowed SF to develop their own a few decades after VOY got back - even if they only had a few hints that the tech exists).
The Tetryon Reactor is what I think they would be working on. That provides a far more interesting way of generating power.
The Thermionic Generators seem to be a form of "Biological Reactor" that depends on the lifeform or living vessel.
That requires far more advanced Genetic Engineering than what StarFleet currently has with their stupid ban on 'Genetic Engineering'. StarFleet might understand the basic principles of how it works, but to genetically engineer a living ship would be asking a bit much of the UFP / StarFleet with it's silly Genetic Engeering Bans.
They are so behind on the "Genetic Engineering" tech that I don't think they could easily catch up.
Pretty much how I saw it. They didn't have to ban all aspects of time travel tech... they could have easily just kept some aspects of it in use and limited it on a hw level to not induce time travel but merely slows/stops degradation in the benamite crystals.
But I still think this issue would have been fundamentally resolved by the 25th century at the latest and using a form of Dilithium Recrystalization technology.
The Recrystalization Tech would be used to grow the Benamite and maybe "Slow it's degradation".
But the eventual usage / destruction of the Benamite through use would be "Unavoidable".
Ergo a constant industry designed around growing the Benamite.
That's definitely how I imagined it.
QS v1 tops out at 300 Ly's per hour which is still VERY fast. But, its 'cruising' speed seems to be much lower, since it was said VOY would have to spend 3 months inside Slipstream to cross 60 000 LY's (aka, about 27.777 Ly's per day). This could easily serve as a replacement for standard Warp drive as its not 'ridiculously fast' but it IS fast enough to traverse large distances in a shorter time frame while using it for exploration purposes.
Voyager was only able to stay in QSSv1 for 1 hr, therefore covering 300 ly's.
The main issuue with QSS is that it seems to do constant damage over time to your ships SIF (Structural Integrity Fields).
And like being super deep under water, if your structural integrity doesn't hold up, your vessel gets crushed like a soda can.
Unlike the Nova Class that can "Quick Recharge" it's shield emitters by turning it off and doing a full recharge in 45 seconds.
Imagine having multiple Shield Layers, each one with seperate shield emitters.
You can have the inner layer "Skin Shields" that are only 1-2 meters away from the hull that form from the grid lines of the ship. Don't push them out into the giant Ovaloid Bubble Shield that we saw in TNG, have it retract back to conform to the curves of the hull to minimize surface area.
Let the "Primary Main Deflector" Dish on the fore of your vessel handle the giant Ovaloid Bubble shield.
Add in a "Secondary Main Deflector" on the aft of your vessel, they can do a quick "On/Off Switch" by turning off the Deflector on the other side and turning on the other Deflector and letting it "Quick Recharge" while turned off.
This would allow ships to constantly cycle between multiple shields and have Multi-Layer shields.
This would require enemies to do "Massive Alpha Strikes" to take you down quickly or be in a long "War of Attrition" like a Pro Wrestling match, but in a Space Battle format.
QS v2 tops out at 10 000 LY's per minute - this can be used (as you said) in emergencies and also as a means to cross the void between Galaxies - Andromeda is only about 4 hrs away at those speeds... not to mention the much closer dwarf galaxies.
From what I can tell, the Benamite Crystals don't last very long, so the useful time limit for those crystals seem to be measured in multiple "Hours", so you could probably cover a very long distance in a short amount of time.
But I would be more worried about getting to a place for a rapid emergency response than using it to cross Galaxies.
We should explore our Galaxy First to 100% completion before we worry too much about other Galaxies.
I'd also rather use Spore Drive to travel the Galaxy, that seems to be a better practical technology to use once you exit/enter the Galactic Barrier, you can hop into the local Mycelial Network like you would hop into the London Tube/Rail Network.