Transporters / replicators / Holodeck make no sense
This is a problem even in the original series, but even more so in TNG, because this show takes place much further into the future.
First, let's think about baldness. THIS MUCH INTO THE FUTURE, and still no cure for baldness?
This opens a Pandora's box full of worms.
We know that transporters work by disintegrating your physical body on a molecular or possibly atomic level, and then magically reassembles it remotely with some kind of invisible energy beam or something, while ALSO transporting your soul and making sure the silver cord does NOT get detached and..
Yeah, when you look at it at almost any level, it makes no sense.
However, let's ASSUME it all makes sense and it just somehow works and dis-, and reassembles your body every time and your soul is also perfectly transported into the NEWLY-assembled body.
Now, WHY would the computers reassemble the body WITH ailments, diseases, baldness, aging, etc.? Why would it ever do that? Wouldn't it assemble the "optimal body" instead of the "old, fat, bald, wrinkled, ailment-riddled one"? There's NO REASON to assemble a bad, pain-filled, disease-ridden, old, aging, wrinkled, fat, bald, etc. body, if you can ATOMIZE or disassemble or disintegrate it EVEN in just molecular level!
Why would they create the EXACT body you had before, when they obviously control either every molecule or every atom! (Where does the energy come from to assemble the body, where are those 'extra atoms' taken from, or are they the SAME atoms (or molecules) the body originally had? What creates the intelligence to reassemble it, does it scan the body into a 'pattern' that could easily then be modified to become the optimal version of a body?)
In any case, when you think about it this way - your every single molecule is detached, there's no WAY anything even COULD reassemble it 'exactly' to what it used to be, but why would anyone want it to, and why would the computers do that? Isn't health important anymore? Wouldn't everyone just be 'optimally healthy' all the time if they had the choice?
Why wouldn't they have that choice with a completely NEW body each time you transport somewhere?
Furthermore, they could IMPROVE the body and they could toy around with different bodies, and when we think about it a bit more, every single transporter would have a huge wall menu of all KINDS of bodies and shapes, abilities and such - heck, there could even be shapeshifter-type bodies that can change into any shape at will! Sky isn't even the limit, since we're in SPACE, way beyond any skies!
No one should EVER be able to transport ANYTHING dangerous onboard, no one should ever be able to transport with a gun, explosive, disease, drug, unregistered entity and so on and so forth. No one should be able to 'hide' anything in their clothes or inside their body - the computer would know everything, since it controls EVERY ATOM (or molecule)! It would by default simply refuse to re-create a gun or an explosive. It could create fluffy bunny slippers for all I care, but it would definitely not create a knife, gun, etc. It would be 100% foolproof.
Someone really didn't think this through when they decided to go the 'teleporting' route for 'transporters'.
Why would anyone ever travel any other way, or die from old age? Also, if someone dies or gets sick, especially 'lethally sick' - there is a cure for _every_ disease. Simply assemble a new body for them - problem solved.
In any case, we should see people switch their body from 'normal' to all kinds of wild things and creatures every single time they use the transporter, because why shouldn't computers reassemble their atoms or molecules in ANY pattern they wish? WHY NOT!?
Where's the imagination?
In any case, even if the transporters can be made to 'make sense' somehow (HOW?), then nothing else makes sense, like dying, disease, aging and so on and so forth.
As far as Holodeck - it would always be occupied 100% of the time, without a second to spare, and there would be SO MUCH demand for it, they would have holodecks everywhere, and eventually EVERY single visitable area would be a holodeck, unless the functionality of the ship would require otherwise.
I mean, why not? It's handy, it's interesting, and you can live much better life that way with interesting, exceptional people and amazing sceneries than with the dullards that are your crewmates or whatnot, on a dull ship.
By the way, this WHOLE series could be just a 'Q having a nightmare' or whatnot; that entity was a mistake, because it's so powerful, it could easily just negate ANY problem in the show, and with a snap of his fingers, he could even remove 'The Borg' from existence. So what's the point of anything, when ALL OF IT could be just Q's prank on Picard..?
So the future is a place with no money and everyone having everything they want all the time, and yet people still sign in and train to be in the academy for some reason.. Holodeck + free food = no space travel.