First things first. Fallout 4 is NOT an FPS, it is an FPARPG (that is First Person Action Role-Playing Game.) Second, Fallout 4 did NOTHING better than other games, only as well as or worse than.
It's settlement mechanics are pretty solid, though the Radiant Quest elements tied into them are abysmal.
The weapon modding system is decently well developed, but fails to really even the playing field, the 10mm will always be better than the pipe gun as a pistol, the hunting rifle will always be better than the pipe gun as a rifle, and the higher-tier weapons just leave everything in the dust.
Power Armor is decently well done, but does not distinguish itself from Halo or Mech Assault 2 (where most of the basic ideas came from.)
The companion system is okay, but has been handled much better elsewhere (like just about any Bioware title.)
The conversation system is almost entirely a bad deal, only the ability to quit conversations was really an improvement.
Dynamic content generation (the legendary loot system in this case) is very weak and could use major expansion, Diablo and other titles have done this in vastly superior ways.
The perk system is almost okay, but really needed some more thought, having to sink 6 levels of perks into lockpick and hacking (three each, with level gating) is a major issue here.
The game itself is not bad, but the majority of its mechanics are weak or half-assed, and those that are strong are not innovative (i.e. they do nothing special.)