I maintain some code (using cronic, see http://habilis.net/cronic/ ) which is sensitive to any noise generated on stderr, treating it as a possible error. One culprit causing false alarms is ssh-keygen, which generates these two messages from around line 1245 of ssh-keygen.c:

fprintf(stderr, "%s updated.\n", identity_file);
fprintf(stderr, "Original contents retained as %s\n", old);

I believe such use of stderr is inconsistent not only with generally accepted use of stderr elsewhere, but with the rest of the OpenSSH codebase. Other non-error messages in that file (e.g. "%s: generating new host keys: ") seem fine with being sent to stdout, and similar diagnostic messages in that file also respect the "quiet" flag, which I would find helpful.

I noticed some other inconsistencies in ssh-keygen.c as well. For example, this bit (line 888) surely should go to stderr instead of stdout:

if (invalid) {
        printf("%s is not a public key file.\n", identity_file);
        exit(1);
}