I still remember the apprehension I felt when I first poked pick into never-before-seen cavern and it's partially-revealed technicolor goodness completely unlike anything above⁑, or especially the creeped-out feeling I got when I first saw a serene grassland moving in the wind (at the time I thought I would never embark in good areas after that look).
Granted, for me those happened in...last spring and summer, I think. I'm not sure someone from 2012 would be able to clearly recall events from around their first few months, but. Mystery and unpredictability are part of it, when the grass looks like it has come alive and is about to murder your entire fortress from all sides while the game is paused.
FBs are intended to be unpredictable, and they are, mostly - description do take away lot of it, as does all being rather big, as does them being still limited to a list, though you still have to check the syndromes from poison fog or dust.
But other part is the attitude you have. If you know the right move in an embark with tower is start prepping right away for the randomly-arriving copper to steel clad siege, if you know you need to dig in straight away in a terrifying embark...Then win or lose, there's much less bite either way - you know it's rng. And ultimately, even the big bad car is just another weapon.
Attitude and experience is what takes mysterious murder investigation for drained body, "why is this dwarf suddenly dead" and makes it a chore to find and kill the vamp.
This requires priming, though, and would take a far better writer than me to properly teach - I just know that random "actually, the mug was coated with contact poison"* can easily be jarring and eye-rolling rather than mysterious.
Now sure, there's still things related to DF rules that are mysterious to me, such as the one in my avatar.
But lets take those away.
In these circumstances, what keeps DF interesting for me is the stories it generates and the simple joy of creating fortresses - often through legends mode, actually, as I research the characters that take on my fancy. Now, wars and conquests and their reasons are also interesting, but most stories revolve around characters - so I wonder what you mean by "species rather than individuals".
As for animal behaviour improvement, well, suggestion forum is open to you.
* Yuli Vasi, if you're reading this, I know it was you and would like you to know with my dying breath that FB tea parties don't work. Ever.
⁑ You can make it more strange an unique if you generate different random underground plants for each fortress/world you play. I think it was Sphalerite who posted code for randomly generating plant raws, but not sure.