Daniel S4? (Spoilers)

[Mitchell82]

Th day-to-day operations of the Atlantis base is under Weir's command yes but it seems thats as far as it goes. You have to remember Atlantis isn't a military base - it exists under the International Oversight Authority, its a research base, its primary aim is to discover new technologies, the miliary aspect came later. Weir was chosen for the job because she wasn't military, so she could act as a neutral party. Military personal would answer to the military first, the IOA second

However strictly speaking, in military matters Weir has little authority, this isn't something new either from the get go the Military were in charge of military matters. In season one Shepperd differed to her out of respect and in season two Weir had the full support of the IOA so she was able to influence military matters (having Sheperd promoted to Lt. Colonel for example). However as the IOA's trust in her erroded so did her influence with the military.

Exactly. Weir had command of the city and the civilian personell but that's about it. As far as any military decisions she had basically no say. Carter has more Military and Scientific experience however Weir has more diplomatic experience. In that respect Carter will have to learn as she goes. I love Daniel and would love to see him on a few eps, but definatly not as a commander.