We discovered that force fields (i.e. electromagnetism) is quantized, giving rise to quantum mechanics etc.

You are confusing quantum mechanics with relativistic quantum field theory. Quantum mechanics was developed as consequence of many different experiments showing quantization phenomena or requiring quantization to explain them, among them the spectrum of black-body radiation and the photo electric effect, but also the quantization of charge and spin. Quantum mechanics and non-relativistic quantum field theory are unable to describe electromagnetic fields, the former because it can not handle the creation and annihilation of particles, the later because photons are always relativistic particles and therefore require a relativistic description. Only with the development of quantum electrodynamics, a relativistic quantum field theory, was a quantum mechanical treatment of the electromagnetic field possible. But this was 20 or 40 years after the inception of quantum mechanics, depending on from where you count.

Matter fields are also quantized, hence their excitations behave like discrete particles - the ones we observe at the atomic scale, for instance.

It is important to understand, that quantum field theory is very different from quantum mechanics. In quantum mechanics a wave function describes the state of a system in Hilbert space, it describes properties of particles. But this runs into problems if the system contains many particles. Two electrons, for example, are indistinguishable and swapping them does not change the state, at least up to a sign change of the wave function which is the difference between fermions and bosons. This complicates the mathematical treatment. And as mentioned before, this approach is unable to handle the creation and annihilation of particles. Quantum field theory therefore takes a very different approach and describes with occupation numbers in Fock space how many particles are in each state.

In consequence the fields in quantum field theory are just a mathematical tool to handle many particle states. We started with particles and introduced fields to describe them mathematically, we did not discover that a field is quantized and therefore looks like a collection of particles. Admittedly this is a contentious issue, there are people claiming that those fields are real and more than a mathematical tool.

In hindsight, we should've been able to predict this after E = mc^2 telling us energy <> matter, thus if energy is quantized so should matter.

We knew or at least suspected that matter is quantized long before we discovered the photon, atoms and particles in general are a very old idea. So at best we could have inferred that energy is quantized from the quantization of matter, not the other way round. But the idea of photons actually predates E = mc², too. You are also probably misinterpreting what E = mc² actually says, you can not use it to link the quantization of energy to the existence of particles, at the very least not in any obvious way. The relationship between mass, energy, and particles is complicated.

And again, I am not a physicist, do not take what I say as the final truth, use it as a starting point. Corrections from actual physicist welcome.