Honestly, Sisko probably shouldn't have been commander of DS9 during the show's run.
For one, we can probably gather that DS9 was not a high priority position. Yes, they were trying to get Bajor into the Federation, but that is more of the diplomats' job than a Starfleet base operator. As others have stated, it was a backwater assignment that really didn't require a lot of Starfleet involvement.
Also, we can gather that Sisko probably wasn't high up on any favorites list at Starfleet. True, he wasn't a troublemaker nor a slacker, but judging from the little we see in "Emissary", he wasn't really an overachiever. He probably did his job as assigned (I suspect the death of his life kinda pushed him into this "coasting state"). This was probably the reason he was give the DS9 assignment. From Starfleet's point of view, it wasn't a high priority, but they wanted someone who was competent at his/her job and would pull it off successfully.
Now, once the wormhole was found, I am surprised that Starfleet didn't pull Sisko out of there right away and assign someone else of higher standing and/or prestige due to DS9 becoming much more important. As I theorized earlier, Sisko wasn't a golden child and, as far as we know, his record wasn't anything too special. Also, he bitched about not wanting the assignment to begin with, even to the point of mentioning it to Picard, the captain of the flagship.
But, if the did that, they would have wasted the entire pilot episode with focusing on a character we'd never see again!
^ Wasn't that addressed in Emissary?
No, it wasn't. The episode ended with Sisko deciding to stay (Wow...job has perks!) and no one questioning it.