Okay, here's my 'in-universe' explanation - but I'll warn you it doesn't paint Sisko in the most flattering, heroic light. Here goes:
Commander Sisko is a faithful First Officer aboard the USS Saratoga living a happy life with his wife and young son when his world is ripped apart by the Locutus lead Borg. He becomes obsessed and unstable in his desire to exact revenge on the Borg. He is none to silent about his feelings toward Picard and is vocal in his opposition in Starfleet's position to keep Picard as Captain of the Federation flagship.
Sisko requests promotion and wants a ship of his own. Because he is viewed as unstable and focused on revenge for the death of his wife, he is denyed promotion and a ship of his own. Instead, Starfleet puts his engineering skills to use by giving Sisko an "out-of-the-way' post helping to rebuild the fleet at the Utopia Planetia shipyards.
Sisko, still obsessed with defeating the Borg, makes the best of this position by designing the USS Defiant, under the premise that he is designing a small escort ship. In reality he is designing the most heavily armed warship Starfleet has ever seen. When Starfleet realizes what he's actually doing, they mothball the Defiant project. They then assign Sisko to Deep Space Nine, the furthest sector they can think of while still keeping an eye on him. His mission is to prepare Bajor, which they consider a long term backwater project, for Federation membership. The time Sisko spends with a quiet, contemplative and spiritual people will do him some good in overcoming his grief toward his wife's death. In addition, his engineering and diplomatic experience on Utopia Planetia and Pelios Station will help prepare DS9 as a makeshift 'starbase' for travelers to the region when Bajor eventually loosens their spiritual beliefs a bit and becomes an official Federation planet.
Of course, everything changes shortly after Sisko arrives - and the rest ...is history.
