Why should one prefer Salsa20 over ChaCha?
I agree that conservatism is the likely reason for the choice in McBits.

ChaCha was published while eSTREAM was still running. Salsa20/12 is now in the final eSTREAM portfolio. Even in the XSalsa paper on constructing a larger nonce, Bernstein makes no mention of ChaCha.


  So what are the reasons to prefer Salsa20 over ChaCha?


Wanting to use a standardized algorithm is one reason. Choosing the more exhaustively studied algorithm is another good one.

If you have your tinfoil hat on, you might also prefer to avoid any tweaks in the absence of real breaks. After all, tweaking the cipher would be an opportunity to introduce new back doors.