If Sisko had been stranded with Voyager instead of Janeway, he would have punched Neelix's lights out in the first episode, instead of tolerating his treasonous behavior on the (dry) planet and kicked him off the ship. He would have likely done the same with the Caretaker (he's not afraid of powerful beings). In fact, the Caretaker would have likely sent the ship back to the Alpha Quadrant for fear of another "meeting " with Sisko. It would have been a one-episode series.
