My personal preferences aside, I'd offer up George Lucas and Tom Hooper as directors who have benefited from collaboration.
I see what you're saying and understand that position, but the film doesn't begin and end with the director. Look at it this way: Direction is a very large part of making a film. Cinematography, writing, acting, sound, editing, etc. are all also part of that equation. To what degree is debatable, but what isn't changed is that all of those factors together make a film. I would say the best film of the year is the one that gets the best out of all those categories together. The director who did the best job can be separate.
Tom Brady can throw for 4000 yards and 40 touchdowns in a season and be the best quarterback that year, but the Patriots might not be the best team, even if he was a hugely positive influence on the overall performance (not a perfect comparison but close to the point I'm trying to make)
I would rather not watch or re-watch any film by either Lucas or Hooper, so I can't agree that collaboration made their films better. I have found them all questionable.
You used a quarterback as an example. I would use a head coach and stick with the same team. The team has dramatically overhauled its roster since Belichick has become the coach, but they consistently rank as one of the best teams in the league. I am sure you would be quick to point out that Brady has always been the constant, but even in his injured year they went 11-5, a feat few teams accomplish each year. Conversely, we have seen great players leave a coach and fail to repeat their success elsewhere. Donovan McNabb and Kevin Kolb looked great in Philadelphia and flamed out elsewhere, while Vick looked like a good quarterback for a few years before it all fell apart.
You can see the influences of smaller parts in films, to be sure. The dialogue of The Social Network was vastly different than what is usually in a Fincher film, thanks to a different writer. Paul Thomas Anderson's The Master was his first not to use the cinematographer Elswit and it had a different look. However, unless you are actually on the set of the shoot, there isn't a real way to say so and so film was directed better but some other film is better. Like the head coach or a CEO of a company, the director gets the credit or the blame.