The Standard Model, which identifies matter and energy as a series of particles, is the current framework for our understanding of how the universe operates at a fundamental level.This is an over-simplified summary, because the term "particle" means something different in quantum mechanics than it does in everyday terms; a quantum particle is not necessarily a small physical object with mass. For example, the particle of gravity, the graviton, has not actually been detected yet, and even if it was, it would have no mass.
One strength of this model is that it has allowed a considerable number of predictions based on the quantized properties attributed to the different particles; for example, the Higgs boson was predicted and, arguably, discovered, using calculations based on a particle model. On a more commonplace level, it is probably easier for humans to conceive of particles than it is for us to conceive of forces, energy waves and the inhuman scales at which these interactions take place. We exist in a world of particles, for the most part, so translating this convention to the subatomic world makes it easier to understand the ways interactions take place.
A downside of a particle model is based in that same assumption; not all things are actually particles. In fact, even matter exhibits wavelike properties. This runs the risk of oversimplifying the model created by a particle system, and making it more difficult to explain wavelike properties. For people working in fields concerned by these issues, this isn't that big of a deal because they already know about the way the model actually works, but for the general public, the over-emphasis on a particle model may create a wall of conceptual difficulty. This also extends to the particle itself; a particle, even those of matter, doesn't have a solid line that distinguishes "particle" from "not-particle" - at the subatomic level, these sorts of certainties get thrown out the window and replaced with probabilities.
There are fundemental problems with any and all models, the first one being size. Making an exact size model of a particle would defeat the purpose as you would not be able to see it. But building a particle to scale presents problems as well. What should you scale it to? A building? A person? Other particles? After you decide the scale to which you want to build your model, you stumble on the problem of movement.
How do you accurately describe the movement of a particle? How could one possibly demonstrate the speed at which electrons or photons move? You can't. We have to settle for scale models of movement too.
Despite these downfalls, models have pros as well. They allow us to see details of things we can't see with the naked eye. They can give us a sense of scale size. In short, models simplify things in order for us to understand the basics.