I would say there is no one right answer here, it depends on the requirements of the system and how well each option meets them. For example the dual converter may not supply the current you want. I'd examine the series option last since depending on the design of the system it could be much more expensive and waste more power: if the 3.3v current is high with respect to the 5v current, your 12v to 5v converter will be needlessly large (and expensive) and will lose energy to power dissipation (inefficiency) that must be added to the loss due to inefficiency in the 5v to 3.3v converter. The dual option is really just the parallel option with both converters inside one chassis, so again the requirements of your system should dictate your choice.
As an example, suppose you are using a 12V motor in a motor control application, driven by a Raspberry Pi and some external logic (such as an STSPIN part). The Pi needs 5V but the external logic needs 3.3. Most of the power in the system is dissipated by the circuit paths that run at 12v. In this case, power usage at 5v would be about 2-3A (for the Pi) and could be much less for the remaining 3V3 logic. Since the 3V3 usage is so low, the 5V supply wouldn't get much larger to accommode the 5-to-3V3 converter so all options are more or less equal in efficiency and you could look at cost or size as your guiding principle. Personally, I'd invest in the best 12V supply I could get since its efficiency will determine the overall project's power usage the most, plus it should have a low output impedance to avoid dirtying the power that must be converted to 5V and 3V3.
