It's a very special feature of $F_2$ that the isomorphism classes of its finite index subgroups are uniquely determined by their index. Geometrically, the point is that an $n$-sheeted cover of $S^1 \vee S^1$ has Euler characteristic $n$ times the Euler characteristic of $S^1 \vee S^1$, so $-n$, and a connected graph is uniquely determined up to homotopy equivalence by its Euler characteristic: every such graph is a wedge of $k$ circles for some $k$, which has Euler characteristic $1 - k$.
Hence every connected $n$-sheeted cover of $S^1 \vee S^1$ is homotopy equivalent to a wedge of $n+1$ circles, so has fundamental group $F_{n+1}$: algebraically, every subgroup of $F_2$ of index $n$ is abstractly isomorphic to $F_{n+1}$.