The reason why equality is only defined for two elements is because it is only necessary to define it for two elements; using transitivity of equality and induction, any statement that $n$ objects are equal can always be reduced to $\binom{n}{2}$ statements that two objects are equal.
A natural definition for a set $A$ of $n$ elements to be equal is that, for all $m < n$, every subset $B \subset A$ of $A$ which has $m$ elements is equal.
Certainly we would want any definition to satisfy this property, so it makes sense to choose this property for the definition.
This leads to an inductive definition of equality of sets with $n$ elements for each $n \in \mathbb{N}$.
For $n=1$, we have from the symmetry of equality, $a=a$, that every one element set is equal.
The definition of equality for a two element set $a=b$ is the standard one.
Now consider an arbitrary three element set $\{a,b,c\}$ such that $a=b=c$.
By transitivity of equality, we have that $a=b$, $b=c$ $\implies a=c$. Therefore, by transitivity, $$a=b=c \iff a=b, b=c, a=c \iff a=b, b=c$$ Similar arguments hold for any $n>3$. In other words, the question of equality for a set $A$ with $n$ elements reduces to the question of equality for all of its subsets with $n-1$ elements, which reduces to the question of equality for all of its subsets with $n-2$ elements, ..., which reduces to the question of equality for all of its subsets with 2 elements. Therefore, we gain essentially gain nothing by considering equality to be an $n$-ary relation instead of a $2$-ary relation.
For an infinite set, we define it to be equal if all of its subsets with finitely many elements are equal (again since any definition of equality for an infinite set should satisfy this property, so it makes sense to choose this property for the definition).
Then it follows that for each finite subset its equality reduces to the question of equality of its subsets with 2 elements.
Thus even for an infinite set the question of whether or not it is equal reduces to whether or not it is equal pairwise, i.e. whether or not all of its subsets with 2 elements are equal, because of the transitivity of addition. Similar arguments will not work for relations which are not transitive.