You are asking about what is known as determinism.
Determinism states "Given the exact position and velocity of every sub-atomic particle in the universe, I'll tell you the origin and fate of the universe".
Heisenberg's uncertainty principle pretty much lays this to rest.
"It is not possible to know the exact position AND velocity of an electron, since measuring one changes the other".
First of all not all the phenomena in the universe are solved by complex equations - some are extremely simple, kinetic energy = (1/2) mv^2, E = mc^2, F = ma... see nothing complicated about them, others of course are extremely complicated, like the Einstein's field equations of general relativity. The equations are as simple or complex as they need to be to explain what they're describing.
As for free will - who says we're different from non-living things? Distinguishing between living and non-living is a question for biologists not physicists. A man chooses to jump off a building, a physicist isn't going to get wrapped up in the socioeconomic-psychological factors that caused this person to want to end his life. Physics asks simple questions from which it can give extremely precise non-subjective answers, for instance:
When is he going to hit the ground?
How hard is he going to hit the ground?
How fast is he going when he hits the ground?
This is in fact a very good analogue for your question, you see before he jumps he has "free will" to choose to jump or not to jump, the second he jumps off the building, he no longer has free will and his fate is passed from the psychologist to the physicist.
Physics doesn't pretend to answer everything about the universe - especially not issues like how are you feeling (leave that to the psychologists) or is there a God (leave that to the theologians and philosophers). What physics does do (and do very well) is comment on that which can be measured and reduce tons of measurements into elegant equations that explain how things are.