Seriously, who actually made the holodecks? Where did they come from?
My head-canon: Holodecks are alien technology that the Federation duplicates without understanding how it really works. Largely-separate power grids. Weird behavior in power outages. Poor safety controls. Different storage technology. Regular accidental sentience.
Holodecks can accurately model unknown physics
TNG’s “A Matter of Perspective” did this first, correctly simulating an energy converter prototype.
Voyager used holodecks in “Threshold”, in order to model warp-ten travel. OK, so maybe this didn’t pan out exactly as in the real world, but why is a holodeck simulation used over just running a simulation? Because the holodeck’s simulation of physics isn’t using the same model that Federation scientists use. It’s better.
Holodecks use very different power systems
Holographic flashlights work in an extreme power outage - in Voyager’s “Night”, the power is drained from everything up to and including the warp core itself… but not the holodeck. More-or-less, anyway - the ceiling lights in the holodeck go off, but the holodeck itself remains functional and holographic torches can illuminate the room!
In Voyager’s “Parallax”, it was found that the holodeck reactors couldn’t be used to power anything else on the ship. Uh… why? Why are they different in the first place? Why don’t Star Fleet engineers already know that this won’t work? Energy is energy, surely - and given what we know about holodecks modelling physics, why can’t a holographic car have jumper leads hooked up to the ship, to pass power along?
Safety protocols are an afterthought
Like it says. Safety protocols seem to fail, a lot, because of other random issues. Where are the safeguards? Automatic program shut-off?
This includes the sorts of protocols that might prevent artificial life. We’re well aware of the possibility here in the 21st century, so there’s no excuse for it two hundred years later. Yet there are so many examples of clear sentience and near-sentience; Moriarty (TNG’s “Elementary, Dear Data”) and The Doctor (of Voyager) are clearly sentient beings, and Michael (Voyager’s “Spirit Folk”) and Vic (DS9’s “His Way” et al) are further close-if-not-sentient examples.
Controls regularly seem to get locked out too, and that results in the program continuing rather than pausing or stopping entirely? Examples start with TNG’s “The Big Goodbye”, continue through “Emergence”, and across the other series.
Other random stuff
TNG’s “Encounter at Farpoint” showed that holographic water can keep you wet after you leave the holodeck. Why? “Sometimes it uses replicated matter” doesn’t seem particularly compelling as an answer.
Also, they can store physical transporter patterns (DS9’s “Our Man Bashir”), though for some reason not the parts of the pattern that includes neural activity?
Why are holographic data streams more reliable (Voyager’s “Message in a Bottle”)? Maybe more to the point, why not use them more often? Voyager had no on-hand holographic data they could send instead of a one-way trip for their physician?
Why is data transfer of holographic programs, so frequently “one-way”? Voyager’s “Futures End, Part II”, “Message in a Bottle”, and “Life Line” all show this.
Did they come from the Xyrillians, seen in ST: Enterprise?
I don’t think so. There’s a ~200-year gap between NX-01 seeing the holodecks in 2151 (Enterprise’s “Unexpected”) and Starfleet deploying them (well after 2293, per Voyager’s “Flashback”).
If they did, my earlier points still stand - the Federation copied the technology without understanding how it actually works.
What about ST: Discovery and The Animated Series?
Yeah, both of these show holodeck-like concepts, but… I’m ignoring them. I get to do that, this is my essay ;). But with e.g. nothing similar being present on the NX-2000 Excelsior, a ship for pushing technical boundaries itself, I think that their presence doesn’t contradict the point above.
The mere existence of them, doesn’t really answer the question about the holodecks - and why after so long, the Federation still has such an arms-length way of integrating them into other systems.