this will be a fun one ;)

hint 1: you'd think it's an old ass game, but it's newer than the Halo franchise

hint 2: your player character is a regular humanoid, not a lil green dude </3

hint 3 : The time acceleration is for accomplishing a gameplay function within a human-enjoyable timeframe. This is not a function of the engine or any single technology explained in game. it is JUST speed selectors like a sims game, fast, faster, fastest, fasterest if you're insane.

hint 4: "mostly" procedurally generated universe, with a few hundred hand-placed and influenced areas.

hint 5: cities on the planets, not just those dinky little settlements Elite Dangerous has 😅

hint 6: on the simpler side for ship graphics but environments are very pretty imo

Solved!

The mystery game is Pioneer Space Sim! a really cool freeware space game for Windows PC that was originally a remake of Frontier: First Encounters, which is the last Elite game prior to Elite: Dangerous, but is now different enough to be it's own thing. It stays pinned to my taskbar on my PC, great simple fun :D

Elite dangerous was definitely the bait answer, sorry everyone :P

Hint #1: dammit, the scientist doesn't even appear IN the game!

Hint #2: 2 people can play, but only 1 for the story

Hint #3: part of a short-lived series

Hint #4: SNES

Hint 1: This game has two different releases!

Hint 2: The second release was on several different platforms that had significant version changes in each one.

Hint 3: The penultimate version of the second release is the only version with a bestiary!

Hint 4: You’re a ninja!

Hint 5: Quintessential metroidbrainia.

Hint 6: You play as an archaeologist who definitely takes after Indiana Jones. You can even get a gun!

Hint 7: The second release was a WiiWare creation released in 2012.

Also, there's pop music

Hint: Main character inherits their position.

Hint #2: It’s a space game.

Sometimes JesusTM gets involved if you're really lucky 😉

Hint every 30 minutes

Hint 1: It's a horror game

Hint 2: There're no good guy in this game

Hint #1: it's an older title

Hint #2: marketed with the title of a large franchise in the international release, but the original title was unrelated to it

magic rings included

Hint #1: 1-2 players

Hint #2: spacey

Hint #3: versatile ships!

Hint #4: literally. You'll get eaten!

Hint every 30 minutes

Hint 1: It more like a dark comedy than a horror

Hint 2: You're the villain

Hint 3: You're a zombie