Seconding Pokemon! The more recent games include regional variations that mimic isolated populations and subspecies, which is really neat. iNat as a whole sometimes feels like going into the tall grass to fill out my real-world Pokedex.
I know there was a lot of conversation around Red Dead Redemption 2, especially with the diversity of the birds included. There were a few articles about virtual birding during quarantine using RDR2. However, I haven’t yet played it myself.
Legend of Zelda: Breath of the Wild has a interesting variety of creatures which have defined ranges depending on climate and location. You even get rewards for running around and taking pictures of each species. You can also find giant cetacean fossils in the desert, implying geological shifts over time, which is a cool touch.
And of course, there’s the Monster Hunter series, especially Monster Hunter World. The actual creatures aren’t all based in reality (though there’s a lot of inspiration from actual dinosaurs), but the whole world feels alive and is populated by a huge variety of species that all have their own niches and behaviors. Again, you get rewarded for capturing and recording information for each creature.
I could probably list more, but these are the ones I can think of off the top of my head. It’s really cool that game developers seem to be putting more time and thought into the natural environments of their games. We certainly appreciate it!