It's kinda nuts that most innovative was between the 90’s and 2000's.
Mostly agree with OP, except Eternal, MGSV and TOTK (even though I loved them all). Especially MGSV feel more 'inspired by' then actually breaking ground. It's a logical continuation of Hitman's clockwork worlds, and Far Cry's outpost structure and tagging mechanics (binocular tagging was first introduced in 2004 with Far Cry 1)
Super Metroid (1993). It spawned a whole search/action genre (now know as Metroidvania even though it's mostly inspired by Metroid)
Speaking of Metroid level design: Batman Arkham Asylum (2009) was a big step forward, especially it's combat systems that still today is being copied in other titles.
Assassin's Creed (2007) was a big leap (no pun intended). From parkour to lived in city feel. With it's towers structure that everyone ripped off (including BOTW)
I would put DOOM 2016 before Eternal. Most indie boomer shooter clearly saw a revival spike after Doom 4 released.
And yeah, pretty much every Looking Glass game is highly influential (even if it's delayed somewhat). System Shock, THIEF, Deus Ex especially. Some might say BOTW is highly influenced by these groundbreaking Immersive Sim's for it structure and systemic approach.
Personal sidenote. Even though I don't care for LOTR, Shadow of Mordor's nemesis system is still so groundbreaking. So unique in fact that WB patent it, the dumbfucks. It's a shame because it would (and still could) be such a leap in systemic emergent storytelling in games. Such a shame.