Magic accuracy and speed penalties were how FO1 and FO2 handled it on a purely mechanical basis as well. Neither of them simulated holding the gun wrong or improper gun lubrication
As I said it extrapolated. There is more going on in a battle then what is shown.
Unlike Fallout 3 where what you see is 100% what is going on.
Fallout 3 did not have the skill penalties outside VATS IIRC. That was a thing added in by mods and NV.
And in NV you also do not see everything. Perhaps your character flinches, pulls the trigger instead of squeezing it or adjusts too little or too much for the recoil or any of those minor things that the devs did not have the time, money or desire to animate. adding flavour to a misfire in olden RPGs was as simple as adding some flavour text to a failed roll. Nowadays, it takes a lot more work to do the same.
You can extrapolate anything from a game if you accept that WYSIWYG does not apply and older RPGs very heavily relied on that, with their isometric perspective and lack of animations (FO1 and FO2 did not have a different character sprite for each weapon. Does that mean that your character magically transformed your G11 into what looks like some sort of a hunting rifle?) and relying heavily on flavour text. The same applies to modern RPGs, even with their abundance of animations and details, some things aren't going to be animated. Though they could have bothered to add in jamming of worn-down weapons.
Anyway, I see this simplified, perk-based system as a step away from pure RPGs. Now I consider this a mixed blessing. On the one hand, it would seem that combat is going to be more like an FPS, relying more on your own skill at shooting than numbers. Which I consider a good thing because the combat in FO3 and NV was this weird fusion of RPG mechanics and first person perspective shooting that didn't really work well at all. Especially in FO3 where your skill in the weapon category only influenced your VATS performance so you had these weird moments when you could shoot everything no problem in real-time but missed every shot while in VATS. So I could see the changes to combat brought about by a mostly perk-based system as a good thing.
Now the actual RPG stuff, I am more miffed about the change of. While it is true that speech, science and lockpicking had set points at which you could do things (except for speech in FO3, which had percentage-based success rates, though the set points were still there), it was a system that more easily lent itself to using drugs and skill magazines (in NV) to overcome what would otherwise be an insurmountable challenge. Now, I don't know how it'll be handled in FO4, maybe they'll roll those skills into SPECIAL characteristics, a prospect that I do not feel happy about since that'd mean you keep what you have at the beginning throughout the game, changing it only very rarely and late-game, or maybe they'll roll it into perks, emulating the "set points of advancement" mechanic of 3 and NV, which begs the question of how drugs, skill magazines and books will be handled and of course why would a player choose the other perks. Either way, I will have to play the game and see.
Also is it just me or have traits been axed? I can't remember them being in the character creation presentation at E3.