Some old games are still pretty rough with their original frame rate. I recently played 4 player golden eye on an n64, and that frame rate was pretty tough to deal with. I had to retrain my brain to process that.

Game design is a big part of this too. Particularly first person or other fine camera control feels very bad when mouse movement is lagging.

I agree with what the other commenters are saying too, if it feels awful at 45 fps your 0.1% low frame rate is probably like 10 fps

Stuttering, but mostly it's the FPS changing.

Lock the FPS to below the lowest point where it lags, and suddenly it wont feel as bad since it's consistent.

EDIT: I completley skipped over that you used Fallout 4 as an example. That engine tied game speed and physics to fps last time I played. So unless you mod the game, things will literally move "slower" as the fps drops.

Part of it is about how close you are to the target FPS. They likely made the old N64 games to run somewhere around 24 FPS since that was an extremely common "frame rate" for CRT TVs common at the time. Therefore, the animations of, well, basically everything that moves in the game can be tuned to that frame rate. It would probably look like jank crap if they made the animations have 120 frames for 1 second of animation, but they didn't.

On to Fallout 4... Oh boy. Bethesda jank. Creation engine game speed is tied to frame rate. They had several problems with the launch of Fallout76 because if you had a really powerful computer and unlocked your frame rate, you would be moving 2-3 times faster than you should have been. It's a funny little thing to do in a single-player game, but absolutely devastating in a multi-player game. So, if your machine is chugging a bit and the frame rate slows down, it isn't just your visual rate of new images appearing that is slowing down, it's the speed at which the entire game does stuff that slowed down. It feels bad.

And also, as others have said, frame time, dropped frames, and how stable the frame rate is makes a huge difference too in how it "feels".

Bro when Majora's mask came out nothing was 60fps lol. We weren't used to it like how we are today. I'm used to 80fps so 60 to me feels like trash sometimes.

The display being at a higher resolution doesnt help either. Running retro games on my fancy flatscreen hi-def massive TV makes them look and feel so much worse than on the smaller fuzzy CRT screens of the time.

I can't stand modern games with lower frame rates. I had to give up on Avowed and a few other late titles on the series S because it makes me feel sick when turning the camera. I assume most of the later titles on xbox will be doing this as theyre starting to push what the systems are capable of and the series S can't really cope as well.

It's a few things, but a big one is the framerate jumping around (inconsistent frame time). A consistent 30fps feels better than 30, 50, 30, 60, 45, etc. Many games will have a frame cap feature, which is helpful here. Cap the game off at whatever you can consistently hit in the game that your monitor can display. If you have a 60hz monitor, start with the cap at 60.

Also, many games add motion blur, AI generated frames, TAA, and other things that really just fuck up everything. You can normally turn those off, but you have to know to go do it.

If you are on console, good fucking luck. Developers rarely include such options on console releases.