* How to set the counters so that counter/IV can't collide and destroy your security
* What metadata your messages need to include to make them not replayable
* How to canonicalize your messages so that the process of packing, authenticating, encrypting, decrypting, and unpacking doesn't change the intent of a message.
I think that may be what the grandparent comment is getting at.
Put another way: find me one crypto library or application implementing CTR mode that got all the above issues right but used a poor block cipher (not AES or 3DES).