I think that Tom's biggest flaw was his need for approval and love from his adopted family. The book delves into this a bit more, even describing a recurring nightmare that Hagen has of being homeless and blind, and his only comfort is waking up in Vito's house. This leads to a unquestioned loyalty to his adopted family and a need for their love and approval. Perhaps this stopped him from being too ruthless, perhaps it stopped him from being truly forceful in his advice to Sonny, Vito and Michael. If this same need drove him as a Don, then he would be a weak one.