For minigames as "games within the game" (e.g., GTA has a lot of these like pool, golf, etc.,) throw another one up for Witcher 3's Gwent!
For minigames as representations of some other mechanic (e.g., hacking, lock picking,) I remember liking the hacking in Deus Ex: Mankind Divided. Reminded me of hacking in EVE: Online.
Probe scanning was awesome in EVE too—at least...it was a decade or so ago. Who knows if it's still the same now doe? Not me.