I’m trying to say, I wish you had been there for me.
Stargate Atlantis “The Siege Pt. III”

(tags from @dedkake)
One intriguing thing about Sheppard is that we rarely get to see him interact with other members of the military establishment. There’s Caldwell, but while Caldwell outranks Sheppard, they have separate spheres of authority (city vs Daedalus) so Sheppard doesn’t really report to Caldwell. Same with Ellis.
There’s also O’Neill and Landry, but the interactions we see are very brief, and despite his rank O’Neill can hardly be considered to be “establishment”. And, of course, Carter throughout season 4 - but, again, Sam’s experiences with the SGC have given her far more flexibility than a CO would usually have. So I think the only two places we see a glimpse of Shepard’s relationship with typical military COs is in his interactions with Sumner and Everett.
And what’s extra fascinating to me is the complexity of those relationships. I think the most succinct way to explain it is that Shep respects their skills and strength of character, but doesn’t respect their authority behind that. He respects the person, if he feels they’ve earned it, but does not respect the office. We see this in how he related to Everett and Sumner, however briefly - but we also see it hugely at play in his relationships with all the expedition leaders, especially Weir. He follows orders because he thinks they make sense, or he trusts the judgment of the person giving them, not because they’re orders.
And even more interestingly - I think you can argue that’s how he runs the team. It’s very, very rare for him to make something an order, and he generally only does it when he really needs to, like with S2 Ronon. (He does it with Mckay once, I think, with the whole RepliWeir situation, and Mckay does not respect that at all, which is a whole other interesting thing). He seems to operate mostly on the basis of earning their trust, so they respect him and his judgment. That’s also why he generally is okay with it when they break his orders (unless it puts them in harms way, or they don’t have all the info). I think it would have been really interesting to explore that more with the military side of the city, and see how they respond to that style of leadership, which is highly unusual for that structure.
atlantistea