The protocol is protected by allowing everyone to run their own full node, to give every user and every entity the power to choose which version of the protocol they want to run. When the network is run by its users, the network evolves in a direction that is best for the users. When the network is run by a few large businesses, the network evolves in a direction that is best for them.
The Bitcoin Core's layered approach is a much better solution than big blocks. The first layer protects the protocol itself, and "big blocks" are implemented on layers on top of that without compromising the core protocol.
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