Do you know what a protocol is? It is an agreed-upon format for exchanging data.
If you expect Russian text describing some action to take, and I send you a poem in Chinese, we are not communicating.
If you expect me to stand on a 12 foot ladder and wave red and blue flags, and I do that, we can communicate.
So, whatever YOU think you can send, in whatever form you can parse on the other end, is a good protocol.
Start with what, EXACTLY, you need to send from one device to the other. "PWM output" is useless information. How much data do you need to send? How often? Sending two integral values twice a month, when neither Arduino has anything else to do means that you could send "two thousand, three hundred twenty four and minus one hundred ninety five."
Sending 4 bytes every 10 milliseconds requires a much more compact representation of the data.