I'm sure there were also games like that out around the same time as HL but they didn't get the heavy PR support. The game engine at the time with it's graphics and physics is what I think helped push it forward.
If Doom 3 was used properly it could have taken HL2s place.

19:25

Asking about HL here should be a bannable offense.

But SiN Episodes: Emergence looks very much like a "Half-Life 2" clone, in turn. ;)

Half-Life is a System Shock clone then.

Deus-Ex
Crysis
Chaser
Prey 2017
Cyberpunk 2077 (the gigs).

I think that in my case, it's simply preferring a different FPS style than HL. There are a lot of games that I only played years, decades even, after release. Some I liked more, some less, some became my all time favorites. Half-Life was somewhere in the middle for me. And I have no real desire to replay it really.

I'd rather replay the first Unreal yet again :).

...

Cryostasis. That's such a perfect example of what you're talking about. First FPS where I felt like a regular guy and not a super soldier.

The first two Bioshocks tick a lot of boxes. Largely linear and story driven. Trapped in a doomed environment. Pretty much straight FPS, but pushing at the boundaries.

The first two Metros are again ticking all the above boxes.

As someone else said the original Prey was really great at this too.

Half Life was the Halo of it's time.
Babby's first retro fps.
Everyone who was into old school fps hated it for ruining the genre.
Doom, Quake, Blood, Duke, Unreal, Marathon, System Shock, Dark Forces fans all considered it inferior.
Only normies liked this tripe.

I started out on Wolfenstein 3D and loved Half-Life. The problem wasn't with Half-Life. The problem was early 3D and its inherent limitations. That then exacerbated by successive console generations prioritising detail over numbers. That's why things changed the way they did. Old school style was unsustainable with publisher demands prioritising aesthetics.

Linear story telling with physics puzzles and guns... Dystopian world with zombies and other unwanted means.

Going off my HL2 memories (So if it's HL1 you're talking about, i don't know), it sounds like most FPS games, though Half-life 2 that i played had a little more physics puzzle and lots of level traversing. The occasional silent dialog with someone after major checkpoints.

Remove puzzles and add more aliens, you get Halo. Add more aliens and horror, you get Aliens Colonial Marines. Add more fun guns, and you get Borderlands. Add more space bending with a companion, you get Bioshock Infinite. Make it a loner in a jungle and you get Tomb Raider (2013).

I suppose it's more the story and how well crafted things are to keep you either guessing or keep you interested more than anything.

Or maybe other people just have different preferences than you? Like enjoying some lore and story to give context to the action. Doom is rightly considered one of the best shooters of all time, but a game doesn't have to play identical to Doom in order to be good.
I think one of the main elements is that these game try to make their world feel lived in rather than existing purely for the sake of gameplay. The puzzles and traversal serve that by forcing the player to interact with the environment, and therefore experience the environmental storytelling, as opposed to just shooting all the enemies and walking to the next encounter. The dialog then serves to add context and explain some of the environmental storytelling you just experienced.

compared to

Doom Z016
and
Doom ZtHlAyAa

This is also a pretty good rule, although I didn't want to run into the problem of "hurr durr, every FPS does that". I don't think puzzles are necessary, since any game can interrupt the flow of the game by throwing in a puzzle, but I suppose it depends on how its presented, in a naturalistic sense at that. Traversal is also something of an iffy subject because it depends if you really consider platforming necessary to the "Half-Life" experience, since some games have a puny jump or others don't even allow you to jump at all, but again, I suppose it depends on the level design.

However, the immersion is a pretty big part. If the game flat out reminds you it's a game by having stuff that interrupts that immersion on a more than constant basis. It's why I discounted anything resembling Call of Duty, the games have too many fail states and it basically holds your hand the whole way (at least the four games I played, I dunno what they did after MW2).

Half-Life was the clone killer. Before it, we had DOOM clones, QUAKE clones, and so on.