I understand that M0/M0 Pro were the arduino.org boards, while the Zero was the arduino.cc boards. But seeing as they are back together, how come all three are now for sale? They all seem to be the same to me.
Additionally, what is the difference between the M0 and the M0 Pro?
The Zero and M0 Pro have the Atmel EDBG chip and a second USB port. The EDBG chip can be used with Atmel Studio to single-step debug. The M0 does not have these features. Additionally, the Zero has different pinouts on a couple of pins. This was likely an error on the M0/M0 Pro but we are stuck with the mistake.
These three boards all are currently in commerce and I don't know what the future holds. In my humble opinion, the MKR1000 and MKRZERO represent the next generation of the Zero and are great deployment platforms while the Zero with the WiFi101 or an ESP 8266 shield is the matching development platform, due to the EDBG chip, and if you don't need to EDBG just go straight to the MKR.
SurfingDude:
the Zero has different pinouts on a couple of pins.
If that is all the M0 Pro and Zero have that is different, why still sell both, why not discontinue one?
Interesting question, I don't know the answer for sure. The two boards do have different layouts and support components, I conjecture that supply chain contracts and inventories for these little parts drive the economics. They are produced in different plants in different countries so shipping and tariffs may be part of it.
A better question would be to ask whether the plethora of Arduino models is of benefit to the community. I can see a school wanting to reuse the same item next term, what with their books already printed with photographs and diagrams. My garden has many happy weeds, someday I will thin it and decide which plants to keep.