Both perspectives miss the point.
You get great movies in both systems. It's just the odds are different.
Woody Allen is an independent. His films are mostly (but not always) funded outside of Hollywood. His content is very independent, he has full control and doesn't ask for opinions from the investors or producers.
The good: Sometimes he makes 'Annie Hall' and 'Vicky Cristina Barcelona'.
The bad: Sometimes he makes 'Scoop'.
And 'Scoop' was atrocious.
Here's the thing -- nobody can sustain genius every time. If you have a true artist on your hands, they'll push the boundaries of a) what's expected and, b) what they're capable of.
Which means they'll sometimes fail, no matter how good they are.
The studios are scared of failure. Especially as they like to spend money. Imagine if Woody Allen directed 'Friends With Benefits' and had final cut privilege. What would happen? Maybe it'd be awful because he doesn't know the lifestyles of the characters, and because he'd rework the script to make the ending less predictable... by doing that he'd alienate all the viewers who just want to see Kunis and Timberlake flirt and kiss.
Or maybe he'd create a masterpiece because he's one of the all time great writer/director's of the New York rom-com. With the studio cash, schedule, and talent; he could achieve great things.
But the risk is too big. (And Woody is a bad example, because he wouldn't ever take that job)
So instead we get a studio made flick which is filtered through producers and studio heads and focus groups.
And sure, the film is likable and many people will like it. It does its job and makes money.
People might enjoy 'Friends With Benefits' but underneath the sweet dialogue and quirky characters is standard formula. The film doesn't transcend. It doesn't change your life. And it never will, because of how it's made.
When you make 'Annie Hall' it might end up being 'Manhattan' or it might end up being 'Scoop'. You just don't know. But when you make 'Friends With Benefits' you make 'Friends With Benefits'. The potential for greatness is blocked, impossible.
The exceptions: Spielberg, Abrams, Eastwood, Tarantino.
These guys rose to the top by being blessed with a touch of genius. Hard work, too, but mostly genius.
They may do work within the studios but they have the attitude of an independent, and the power. Spielberg is like an excited Kid, Eastwood has exquisite instincts, and Tarantino is an obsessive maniac.
They stand out as unique and independent spirits.
That's what you need. If you make independently funded films based on things you're passionate about, the door is open for greatness. But it's also open for disaster.
Working in the studio system safeguards against disaster as best as it can. But you only get to make art if you rise to the top by being marked with creative genius and an ability to pull in giant audiences.