I would like to just briefly get into what is missing, from the Standard Model and point out where it falls short of being a complete theory of particle interactions.
Origin of mass
This is the issue of mass generation. Part of the reason that this problem is so difficult, is, that the issue of mass, is so closely tied to the gravitational interaction, of which there is no coherent consensus on how it is to be integrated into the Standard Model of particle physics. There are models of mass generation that involve gravity and some that don't.
Strong CP problem
This is the question of: why does quantum chromodynamics, not violate CP-symmetry. CP-symmetry is a combination of C-symmetry and P-symmetry.
C-symmetry or charge conjugation symmetry is when a particle is interchanged with its antiparticle.
P-symmetry or parity symmetry is when the spatial coordinates of the particle are flipped or mirrored.
Indeed, according to quantum chromodynamics, CP-symmetry should cause a violation in the strong interaction. However, such a violation has yet to be experimentally observed. This is an unsolved problem.
Neutrino oscillation
This is when a neutrino, measured to have a specific flavor at one moment, is seen to, at another moment, be a different flavor. This phenomenon has been observed. However, the theoretical aspects of the process are not yet fully understood. The big problem with neutrino oscillation, however, is that it would require that their non-zero mass, predicted by the Standard Model, be modified.
Baryon asymmetry
This is the imbalance of everyday baryonic matter with antimatter, as observed in the universe. The natural assumption is that their should be a balance between the two, however, physics can’t provide a meaningful explanation for why this is the case. Indeed, the Big Bang, should have created equal amounts of matter and antimatter. There is no consensus yet as to why there is this imbalance.