Most of the rest of OpenSSH seems to have moved over to protocol 2 keys by default (e.g. ssh-keyscan did so recently). I think ssh-copy-id should do the same. Patch attached.
Created attachment 1551 [details] change ssh-copy-id default to id_rsa
patch applied - this will be in openssh-5.2. Thanks!
Close bugs fixed/reviewed for openssh-5.2 release