Which should be the perfect protocol and why?

aq_mishu:
See, thus it's like a multi master type (in my eyes). Consider it like a multi task and each task has a different sub controller.

People often come to the Forum with a concept in their head that is far more complex than it needs to be - usually because there is insufficient definition of what actually needs to be done.

I don't immediately see why the scope outlined in your Original Post can't be handled by a single Arduino Mega.

On the other hand you say

consider it like a inter motherboard with bios, RAM, bla bla bla... I mean several subsystem will make a interconnected network inside the board.

and that makes me wonder if what you really need is a RaspberryPi or a cheap laptop.

"Motherboard". "bios" and "RAM" (in that context) are not what an Arduino is intended for.

...R