Following on from here, I am unconvinced that encrypting twice with RSA is a waste of time: doesn't it depend on what is placed in-between the two encryptions?. What would happen if a permutation was applied at this point? How strong will the encryption be then?
That is, $$f(m^{e_1}\mod n_1)^{e_2} \mod n_2$$
I am not 100% familiar with the RSA algorithm, and so am unsure whether $n$ could stay the same in two different encryptions using different keys, so have used $n_1$ and $n_2$ (perhaps we could have $n_1=n_2$ if this is ok).
To choose $f$, perhaps someone could use something else like a different symmetric algorithm or, even better, have the (symmetric) mapping function sent to the recipient encrypted using the 1st RSA enryption (that way he can change the mapping whenever he wants - even when sending the same message to many recipients).