But now let's divide each element of E by 2 to produce a set D. Now that set D is {1, 2, 3, ...} aka N the natural numbers. But we just applied a function to each element of E, so how can D have a different size than E? Each element of E maps to exactly one element of D: 2 -> 1, 4 -> 2, 6 -> 3, etc. So does size(D) = size(E)? Or does size(D) = size(N)?
I imagine you're right that this leads to a contradiction somewhere, but I (obviously) haven't thought it through. I just would love to see someone try to break enough axioms to make it work and see what comes out of it, or show that it contradicts either itself or something we see in the real world if we do that.
But yes, the ordinals might be more to your liking. If you equip your sets with more structure you can say more things about them.
You are assuming that this doesn't change the size and certainly that's how the normal notion of size works. But the question is whether we can create any order relationship on the sets with the desired properties.
The properties he mentioned defines a partial order and partial orders can be extended to total orders (given axiom of choice). So it is in fact possible.
But a partial order of all sets? How is this function "size" even defined? Functions don't have a domain of all sets in conventional set theory.