Civilization IV: Caveman2Cosmos mod & Age of Wonders III
Build your way up through the ages, starting from baseline neanderthal humans, but once you reach a certain point in the Ancient age, you have a choice: Magic or technology?
Magic has the potential to mutate your civilization into entirely new species, and is extremely powerful to start, while technology starts out weak but steadily gains power. Early ages has magic and religion potentially tied together quite strongly, with huge benefits, but as the world ages and more becomes certain about how the world works, magic slowly starts to fade, paving the way for technology to start to shine.
Of course there will be ways to accelerate or attempt to prevent this process, in one direction or the other. Technology doesn't work well in the presence of magic or vice versa, as magic breaks the physical laws that machinery requires to run (so I guess a little bit of Arcana as well), so hybridization is difficult if not impossible. Enough study into the ways of magic may yield methods of bringing the world to a more primal state, with magic having greater (but often unpredictable) effects, and technology becoming weaker, while technology imposes a state of order on the world that causes magic to fizzle out.
If they manage to maintain a state of equilibrium, then you could potentially end up with dragon riding elves fighting off F-22 Raptors, magical depopulation bombs vs conventional nukes, giants vs tanks, modern infantry against zombie hordes...
...I actually kind of want this game.