Right from the get-go, Sipowicz never gave respect to anyone that he didn't feel deserved it. Now, some earned his respect, but Sipowicz is someone who never had a problem going his own way and doing things the way he thought were best. Anyone who thought that Andy was just going to "fall in" are those who never knew the character.
Of all the people in charge of Precinct 15, it's hard to believe that anyone else would have gone against the brass of 1PP, especially within days of assuming command. The only other officer I can think of who might have would have been Lt. Fancy. Sipowicz, however, doesn't even hesitate because he trusts the instincts of John Clark and the other detectives that something isn't right when a Japanese diplomat signs a confession to the murder of a prostitute while another wealthy man--under the guidance of his lawyer and a chief of the New York City Police Department is suddenly in the clear.
One of things I've always loved about Sipowicz is that he has no compunction going against anyone, especially when he knows that they are wrong or that something is off.
The other thing I've always loved about Sipowicz is his unswerving loyalty to those he works with. He will always have their backs no matter what. And it's THIS quality that makes him the guy that anyone would want to work for. How many times throughout the series have we seen Andy go out on a limb for someone? More times than I can count. You don't necessarily want a guy who's always going to follow orders, but you do want someone you know is going to have your back.
While Sipowicz may have doubts about assuming command of 15 squad, nobody else does, least of all the audience who knows him only too well. He's PERFECT for the job. Knowledge, experience, dedication, loyalty, and the tenacity to always do what's right (especially for the victim)--who else embodies these traits better than Andy? As the audience, we already know the answer to that question.