atomic theory is extremely well accepted and not up for debate in any way.
here's the difference between chemistry and physics:
chemists care about the properties of materials at the length scale from micrometer to angstrom - the size of a bacteria to the size of an atom. this is the length scale that quantum mechanics starts to dominate, and in my opinion more importantly, where behavior is significantly influenced by thermal fluctuations. This is the scale where everything in chemistry happens: solvation, foaming, reactivity, diffusion, self assembly, protein folding, crystallization, etc. Chemists apply this knowledge to design things that require molecular, nano or micro level precision - new nanomaterials, thin films, medicines, sensors, semiconductor processing techniques, medical implants, etc.
Most of the "easy" theory in chemistry is already taken care of. The "hard" theories remain but they're not things that beginners would even understand why it is a problem. These are things like the biopolymer folding problem, abiogenesis, the scaling problem (why do molecules of foams, micelles, proteins, etc. assemble into higher level structures and how do we predict the transition point?) which are extremely specific and hard to answer. For example we have surfactants that, at low concentrations, just dissolve into water. but at higher concentrations, they start forming micelles, and then assemble into surface foams. How do we predict, without doing any experiments and just using a computer and theory, what that critical concentrations are and what the entire mixture looks like at any given point? Or, how do we predict, without doing any experiments, what the structure of any arbitrary protein is?
physics care about ALL length scales, and ALL properties, not just those of materials. for example physicists study black holes. that's on the kilometer-light year length scale and a black hole is not made of any material. they also care about far smaller things like quarks, which are useless in chemistry.