One of the fun things about baseball is that fans are so familiar with all of the tactics and levers to pull. Things basically happen one at a time - it's not like the other sports where all the players are moving at once. It's easy to want to pull a bunch of moves - and think along with the manager.
Bobby Cox, Francona, Earl Weaver (all great managers in their time) - all got harangued I think for not bunting, not hit and running ... for more or less (usually) let the players play. Of course, that is (in general, if the players are good) the right thing to do. Also managers are like any other job - they can get better. Francona and Bochy have.
I'll use Francona as my soapbox - although Bochy and Maddon certainly could be advocated if you wanted.
1. Created a comfortable work environment. He resembled (to me) a good manager at a real job. Made great pains not to humiliate his players. Not every player thrived, but that happens with everybody. Managed one of the more ego-filled clubhouses you will every see, and got people to pull in the same direction - a lot of times just by being a remarkably decent man.
2. Managed coaches - The Red Sox staff turned over a lot over that time. Lot of coaches came through, but the overall quality on that end did not suffer.
3. Managed the media - He was effectively the Red Sox Press Secretary. He represented the Red Sox as a corporation wonderfully.
4. Integrated young players - Supervised one successful transition of players. When the GM wanted to usher out vets and play younger players, Francona could do that too. He gave the kids playing time, defended them in public, while developing and holding them accountable. Pedroia (example I always go to) was handed the 2B job without much big league evidence in his corner, but was given the time to breathe and grow into job while not compromising the big league mission. I think his background in both managing, and player personnel helped.