i think that people miss one component to the Mafia. Cooperation!!!.... Bonanno wasn't technically in line to run the after the Maranzano hit. Angelo Caruso was the underboss and represented the old timers but Bonanno because of age and his primary business (bootlegging) was probably more accessible to the likes of Luciano, Costello, Anastasia and the new order.
there was another Maranzano guy vying for position named Francisco Italiano. He was made Consiglieri but was whacked several years later. and if you research, after the "end" of the Castellamarese war, in all five families, many guys were whacked for residual issues from the war but mainly for not cooperating with the new order.

Bonanno could be worked with, plus he was a known Maranzano bodyguard with a strong familial faction, plus ties to the Boss of Buffalo......