I like Sisko a lot, possibly being my favourite captain. Avery Brooks is certainly a divisive actor though. I'm just on a series rewatch, and I forget how much it took Sisko, Bashir and Dax to settle into the rhythm of the show. Sisko and Dax in particular had issues with the acting as well as the writing.
Gradually, the producers wrote more to suit Brook's persona. By season three, Sisko came into his own. And of course, by the time he's bald and bearded, he's also totally badass.
He's not the best actor the franchise ever hired, yet he has had so many emotional moments that I remember. I agree that his best scenes were often with Jake.