I'd say from the most fundamental point of view we have today particles are described by quantum fields. It's indeed important to keep in mind that the particle-like phenomena are due to the interaction of quantum fields with the macroscopic measurement devices (which themselves are, at least in principle, many-body quantum-field theoretically describable systems). E.g., photons (i.e., single-quantum-Fock states of the electromagnetic field) have no position observable to begin with. When detected with a position-resolving device (on a fundamental level usually somehow related to the photoelectric effect), it appears as a localized excitation of the detector material, but that's no contradiction but well understood.
The didactical question, how to present quantum theory is however unsolved for me presonally. I'm a strong proponent for the non-historical approach, starting with simple phenomena, presented from the point of view of modern quantum theory. The problem with this approach, however, is that it's hard to start in this way because if you want to start with the Stern-Gerlach experiment and spin-1/2 two-dimensional Hilbert space, you don't have the notion of spin at hand since this needs the very notion of modern quantum theory to get it right. In the previous semester I have given an introductory QM lecture to physics-teacher students. There I decided, I use the polarization observable of classical electromagnetic wave and polarization filter ("polaroids foils") as heuristic starting point for the description of idealized von Neumann filter measurements, introducing the photon in a quite qualitative way, but emphasizing that the naive idea of localized particles is flawed and that rather the wave picture is a better heuristics but also not completely correct. From this you can build the fundamental idea of modern QM to use a Hilbert space to define states and observables with the minimal statistical interpretation for the physical state (a la Born). In my opinion the interpretational problems of quantum theory (if you agree that there are such problems, which I doubt as a physicist, but that's a personal opinion) can only be discussed after a thorough mathematical introduction to the theory. There's no way to do QT (if not even physics as a whole) than this solid mathematical foundation.
The historical approach is particularly bad for introductory QM, because it overemphesizes the wrong concepts of the "old quantum theory", i.e., Einstein's flawed particle picture of photons and Bohr's self-contradictory atomic model with discretized classical orbits of electrons around atomic nuclei. The problem with this is that the pictures are not only empirically wrong (except for the energy levels of the hydrogen atom and the harmonic oscillator, which systems are so restricted by the huge dynamical symmetries of these special systems that it's almost impossible to get them wrong in any reasonable theory, there's no single other successful application of Bohr-Sommerfeld quantization) but provide wrong qualitative pictures about what's going on on the quantum level. The only way to get intuition is to get used to mathematical thinking and its application to the quantum phenomena.
Don't get me wrong: I also think that some knowledge of the history of physics is very important for any physicist, and it's of great merit to study it, but it's the wrong way to introduce physics in the intro theoretical-physics lectures. After you have learned the modern theory, it's however very good to study how the physicists came to these theories and models as a result of an interplay of experiments and model building by theorists.