I think the writing had still a lot to do with it. From what I can tell, Brooks was very much interested in the father-son relationship presented in Emissary, and I think it shows during any scenes he had with Lofton. He could also be strong in his scenes with Farrell, where the characters were reliving their past histories. I think he was there for the paycheck. Indeed, he was still teaching at Rutgers concurrently with the show, sometimes filming lessons while in uniform.This actually explains a lot. Sisko always seemed to be more than a little aloof in the early seasons. I always thought that was part and parcel of the writing (which, in the first two seasons, really left a lot to be desired), but it makes a lot of sense that Brooks' lack of passion would have a deleterious effect on his character and the show. I wonder what it would have been like if he'd actually brought his A-Game... Although, in fairness to him, I can't imagine it being all that exciting as an actor to find oneself playing Alien-Hop-Scotch. Like so many of us, he probably just went to work, did his job as a professional, collected his check, and went home in the evening to do something that was actually rewarding.
IMO, any lack of effort on Brooks part was more symptomatic of the show as a whole. That first season feels like TNG-lite in many respects. Piller very quickly started calling for a change in direction, which led to Duet and In the Hands of the Prophets. In Season 2, he pushed harder for the show to be different. Odo became more prominent because Auberjonois was disgruntled at the direction of his character. By mid-season two, there are efforts to explore more of what made Sisko unique. If anything made a big difference, it was making Behr the showrunner. Among all the elements he introduced, he made the writers attend performances of Brooks one-man show about Paul Robson: he wanted them to see not only what Brooks was capable of, but what motivated him.