Let $A(e_1,e_2)$ be the number of spanning subtrees of $K_n$ containing both $e_1$ and $e_2$.
We want to minimize $A(e_1,e_2)$.
If $e_1$ and $e_2$ are adjacent then we can count exactly how many trees have $e_1$ and $e_2$. To do this contract those edges into a single vertex $v$, for each spanning tree in the new graph with $n-2$ vertices there are $3^{d(v)}$ spanning trees on all $n$ vertices.
So using the prufer code we can see there are $\sum_{i=0}^{n-4}3^{i+1}\binom{n-4}{i}(n-3)^{n-4-i}$ trees in total.
If $e_1$ and $e_2$ are not adjacent then we can also count exactly how many trees have $e_1$ and $e_2$ exactly, we do the same trick (contract each edge into vertices $v_1,v_2$), but now we notice that for each spanning tree on the new graph with $n-2$ vertices there are $2^{d(v_1)+d(v_2)}$ spanning trees on all $n$ vertices
So using the prüfer code we can see there are $\sum_{i=0}^{n-4}\binom{n-4}{i}2^{i+2}2^i(n-4)^{n-4-i}$
Since there are $\binom{n}{i}$ ways to pick the $i$ vertices that are $v_1$ or $v_2$ and $2^i$ ways to split them (between $v_1$ and $v_2$).
So all that remains is to compare:
$\sum_{i=0}^{n-4}\binom{n-4}{i}3^{i+1}(n-3)^{n-4-i}$ and $\sum_{i=0}^{n-4}\binom{n-4}{i}4^{i+1}(n-4)^{n-4-i}$
But using the binomial theorem, the sum on the left is:
$3n^{n-4}$ and the sum on the right is $4n^{n-4}$, so the left is smaller.