A poser on Presidential/Congressional Powers

Mom asked a really good one, today: How long, exactly, has it been required of the POTUS that he gain approval of Congress for the appointment of field commanders? Isn't he the Commander In Chief? Doesn't that, ostensibly, grant him the power of promotion at the highest levels? How's come Petraeus had to be approved by Congress in order to replace Casey?

I understand that Casey need Congressional consent to be made Chief of Staff... but isn 't the rest of this business the President's Constitutional turf? Or does it fall under the Legislative section by virtue of the following section of Article 1? :

To provide for organizing, arming, and disciplining the Militia, and for governing such Part of them as may be employed in the Service of the United States, reserving to the States respectively, the Appointment of the Officers, and the Authority of training the Militia according to the discipline prescribed by Congress;

Has this really been the standard practice all along, and we've just never noticed it until Dubya took command and the rancor got turned to "eleven"? Or is it relatively new?

Wow, I really haven't been paying attention, have I?