Star Wars: Jedi Knight: Dark Forces II (PC, 1997)

Wireframe map that fills in as you explore (2D top down view, like Doom except this one doesn't have a separate screen) plus additional 3D map in the menu (rotatable and zoomable)
Some alternate paths through levels
Persistent item and weapon inventory (Strife)
Many secrets (finding all secrets in a level gives you one more point to put into force powers) and small semi-hidden detours for items
Quicksave anywhere (but no quickload, many nameable save slots)
Choose between a light side or a dark side path ~2/3 into the game (affects the ending and later force powers, killing NPCs will gradually move you towards the dark path (except for a friendly droid in lvl 4 which takes a lot of hits to kill and will trigger the dark side path if you do it)
Jedi force powers (some of which affect how you can traverse a level) and a basic skill tree system for them (unlock powers and points to put into them as you beat levels - can save points for later)
Resource management is pretty important (limited ammo for every gun, you'll quickly run out of ammo if you only use the rapid fire guns)
One escape sequence (kind of confusing layout for the level but there are two different solutions as you can use force speed+force jump to get to the other side if you took the wrong path at first)
Levels feel more like actual places overall without sacrificing gameplay (in general - sometimes gameplay takes precedence and the level feels pretty arcade-like)
Lets you ambush some enemies (enemies tend not to react to any noise but laser fire so stealth is basic)

Playthrough - Mini Review

Influenced by: Probably Duke Nukem 3D, Tomb Raider, possibly Strife, Shadowcaster, Hexen, Powerslave/Exhumed, The Divide or Daggerfall (map system), 

Influenced: Possibly Half-Life (jump upgrade, NPCs), Metroid Prime (map system), Requiem: Avenging Angel, Star Trek: The Next Generation - Klingon Honor Guard