I am wondering if my experience of Prey -- which I admire greatly -- is a common one or if I am simply not playing it "properly". I am in the Restore From Backup mission, so two-thirds of the way through and I still feel inadequate! I have missed finding certain weapons like the Q-Beam emitter, I am often perilously close to running out of ammo for the weapons I do have and I am certainly learning that some, if not most, enemies are best avoided rather than fought! I realise this is part of the game's design and I appreciate it but I do spend a lot of time sneaking about knowing that I do not have the firepower to take on the Phantoms and Telepaths, etc. I even have a hard time with the rogue Operators sometimes. And the stupidest thing I've done is dump my Boltcaster by accident after clearing out my inventory; I might have to go back to the Crew Quarters to fetch it!

I have missed so many opportunities, bungled so much and died so often that I thought I might even restart the game but I'm actually making progress, albeit struggling to stay well-equipped. As I said, I admire this game and know that it's not a straight shooter; the player is the Prey. However, am I playing it "wrong"?

It sounds like you haven't explored very much, as there's multiple Q-Beams lying around. I think at least 4, by the point you're at. Hardware Labs, The Exterior, Crew Quarters, and The Guts. There's a 5th one in Cargo Bay. If you're low on ammo, you should be fabricating more. If you can't fabricate, then it's because you haven't recycled enough. Need more junk? Explore. You should also try to extend the value of each shot - upping damage. Combat Focus, the Stungun, Nullwaves, and Gloo all add damage bonuses to enemies, often cumulatively. A fully upgraded shotgun, with Combat Focus, Sneak attack damage, and a critical hit, can even kill Voltaic Phantoms in 1 shot on Nightmare difficulty. Obviously that requires some luck Ultimately, I'd suggest exploring more, getting more Neuromods, and perhaps reloading some saves to test which weapons best work on which enemies.

Personally, I've never snuck past any enemy. But I also find the Typhon abilities to be extremely underpowered and disappointing. My shotgun can kill the Nightmare on Nightmare without reloading.

Here's all the junk in the game, just prior to the last missions. Just to give you an idea. https://imgur.com/a/SZBuu5B

The game is only difficult right at the start, when you still have no neuromods or good weapons. Also avoided the pre-order Shotgun so only had the wrench/pistol for a pretty long time. Was playing on Nightmare but still, by the mid-point of the game, it was extremely easy to just roll through anything. Basically, the moment you find the Neuromod fabrication plan, you've won the game. Then you just do a clean sweep of absolutely everything lootable on the space station and transfom it into skill points for a massive power spike. Would have honestly been better if Neuromod fabrication plan wasn't a thing. You overcome the difficulty curve extremely fast as it's pretty much static but you power level keeps growing pretty fast. Combat Focus is such an extreme overkill that I refrained from using it (generally hate slo-mo in single player FPS games), but might help you. It's cheap both on skill points and Psi and is basically an "I win" button.

Also, exploit operators. They really should have had limited uses. All resource management goes out the window when you can just run back to an operator and have everything, health, armor and psi freely refilled whenever you want. You should only be using inventory resources when absolutely forced to during combat. It's a waste otherwise. Using Psi-Hypos especially. Their best use is to be recycled to be transformed into skill points.