Another issue with Sisko's command is that it's divided between the Defiant and Deep Space Nine.
It makes sense for the narrative in order to center things around the characters. But, if you're looking at it practically within the reality of the show, there probably should have been a separate crew just for the Defiant.
Especially after Deep Space Nine becomes an important strategic position, it doesn't really make sense for Sisko to be light-years away on the Defiant with most of the command staff on some mission, leaving Deep Space Nine to be guarded with a skeleton crew.
To that end, I always found Kira's presence on the Defiant peculiar. Even before the Dominion War, she's a major/colonel in the Bajoran militia going out into deep space on Starfleet missions that have nothing to do with Bajoran interests.
Kira being on the
Defiant made sense more often than not. Looking at her appearances on the bridge of the
Defiant before the Dominion War...
"THE SEARCH, PART I" - that mission would directly affect Bajor, as the wormhole is in their system.
"PAST TENSE" two-parter - Kira being one of the only direct witnesses to seeing the Founders, plus how a symposium talking about the situation in the Gamma Quadrant also affects Bajor. Almost certainly was invited to the symposium.
"THE DIE IS CAST" - Odo IS a member of the Bajoran security force and under her direct command.
"THE ADVERSARY" - this one is hard to defend.
"STARSHIP DOWN" - also hard to defend, but there may have been some Bajoran interests with the Karemma trade.
"PARADISE LOST" - also hard to defend, but Worf was in command there.
"SONS OF MOGH" - Sisko ordered her to take the
Defiant to find out what was going on, plus since it was a situation potentially directly involving the Bajoran system.
"RULES OF ENGAGEMENT" - possibly her experience with Cardassians, since they were escorting a convoy into Cardassian space.
"TRIALS AND TRIBBLE-ATIONS" - they were picking up an Orb. Definitely justified being there.
"FOR THE UNIFORM" - as damaged as the
Defiant was, it really was an 'all hands on deck' situation. Plus, she knows the Badlands.
"IN PURGATORY'S SHADOW" - Sisko ordered Kira to take the
Defiant into the Gamma Quadrant to see what was going on.
"BY INFERNO'S LIGHT" - this is a no-brainer. The Dominion fleet was threatening Bajor.
"CHILDREN OF TIME" - hard to defend this one.
Out of 14 times, only 4 are hard to defend, with one of those at least having a possibility.