Electronic – Using a voltage regulator to power MSP430 microcontrollers

If power requirements are low (tens of millamps) I tend to use linear regulators. It doesn't matter whether you go from 12V to 3.3V immediately, or via 5V, the efficiency is the same (and rather bad). Make sure, however, if you use a regulator to go from 5V to 3.3V to use an LDO; the voltage difference is too small for standard regulators.

If you want to use SMPSs you'll have to look at the efficiency. This is in general lower for lower output voltages, and also if the Vin/Vout ratio gets higher. Let's say you go from 12V to 5V at 90%, from 12V to 3.3V at 80% and from 5V to 3.3V at 95%. So going from 12V to 3.3V in 1 step will be 80% efficient, if you do this in 2 steps (via 5V) your overall efficiency will be 90% * 95% = 85.5%. You'll have to make the calculation for your specific regulator.

If you're confident that the battery voltage remains within the MSP430's specs you don't really need the regulator, but I would recommend to use one to have a clean power supply voltage. In any case, be sure to have a look at other components the MSP430 connects to. For instance when you drive a MOSFET the gate voltage may be below pinch-off and the FET won't do its job.
(I don't quite remember the specs, but I once tested how low the MSP430 would go, and found that it still worked at 1.3V. Don't take this value as a reference, though. Always refer to the datasheet!)

If you want to measure the battery's voltage you'll need an ADC reference voltage that's independent of that. For instance use an LDO to create a fixed ADC reference voltage of 2V, and divide the battery voltage by two before applying it to the ADC (to make it lower than the reference)