Transporter (etc) makes no sense
All this 'holographic energy stuff' makes no sense, really. I have written a bit about how replicators and the holodeck would change the attitudes, minds, lifestyles of people so much, this kind of space travel probably would never happen, but the one BIG problem in all the Star Trek shows and movies is the transporter.
I am all for 'materializing' things from pure energy using some kind of higher-level 'blueprint', so you can tell the computer go give you Earl Grey Tea (though I would rather go for Green Tea or Maccha - and I refuse to write it 'Matcha', because it makes no sense in hiragana). No problem with that.
However, when you take something that already exists, then disassemble them on atomic level, then recompile the atoms, we run into massive, MASSIVE problems and implications that ripple throughout all existence.
Just off the top of my head; what would happen, if the computer malfunctioned, and suddenly transported Q somewhere, but failed to reassemble him? Of course, an omniscient entity would see it coming because they can 'see the future', but what would technically happen there?
People of this planet, especially writers of TV shows, have not yet figured out how a human being REALLY works, what life REALLY is and so on. They think a soulless fetus is 'human', they think removing a lifeless blob from a womb is somehow 'murder' and so on. Sigh.
A human being is not the physical, bipedal entity you see in front of you. It's the soul that INHABITS the physical body, not the body. You have a body, you are not a body. This kind of super BASIC info seems to be lost in this world for some reason.
But we can disregard ALL the deeper knowledge about chakras, meridians, akupoints, the etheric body, the astral body, the silver cord, mental body, causal body, the soul, energy vibrations and so on - how ALL that would work with a mechanical 'transporter', is quite puzzling to think about, but fine, let's SHOVE it all aside.
My point this time has to do with the age-old, puzzling question; if an entity is disassembled completely into atoms, into a 'pattern' (I am trying hard to not ask where the soul is when this happens), and then reassembled again into EXACTLY what they were, including their clothing, weapons, etc., then..
01) ..shouldn't it be 100% impossible to sneak any kind of weapon or bomb into Enterprise? This seems to happen, and 'mystery objects' are 'transported', but the TRANSPORTER COMPUTER should know EXACTLY what is in the box, or it could not reassemble the atoms, now could it?
02) ..shouldn't the reassembled version of ANYTHING be 100% pristine, clean, healthy, perfect? Why would they take a faulty heart and reassemble it EXACTLY as a faulty heart, when they could reassemble it as a healthy heart? Why would ANY illness exist, why would anyone get older, when they would be reassembled as their optimal, most healthy, virile, youthful 'self' every single time they use this thing?
This realization makes it hard to swallow things like 'beaming up injured parties' why would the transporter reassemble someone injured, EXACTLY as 'injured', instead of 'completely healthy'? Why would it EVER do this? There should at the very least be a confirmation dialogue, as in 'This bipedal entity has a face scar - are you sure you want to reassemble them as injured in the face? Y / N?' or something.
It also makes you think about so many things, like Riker's beard. How easy would it be to never have to shave, and always being able to 'grow' a full beard instantly, because that 'pattern' exists in the transporter and you can customize your look to bearded or non-bearded every single time you use the transporter? You could have a 'default setting' and then perhaps a planetary customization, so you'd have blue skin if you materialize in planet Goosbane and so on.
Cosplaying would be super easy this way, and it, of course, could, and realistically, WOULD eventually (if not immediately) manifest towards people wanting to customize their physical body more and more, until we'd have TRUE 'furries' and My Little Ponies and all kinds of weird, odd-sized, animal-, and other creature-shaped people running all over the place!
WHy would anyone ever WANT to be in a dull, samey, predictable bipedal entity body if they could be a different creature form every time they transport? Why would they want to do a dull 'space exploration' (which amounts to bringing medicines to different planets or boringly try to push some moon to a different orbit.. the title lies so much, 'explore different civilizations', 'go boldly where no MAN has gone' MY A55! All they do is 'side quests', the interesting stuff happens as a coincidence every time!)..
..when they could play around with this form-changing stuff and even duplicate themselves as some kind of half-transparent, rainbow-colored squirrel-trees and marry themselves as such?
It's MIND-BOGGLING, how many absolutely massive implications this transporter stuff has..