Yes, those two "average guys" know how to make a story their own and tell it in a unique way while dealing with the compromises and challenges of a studio system. Their films remain highly personal works with their own stamp upon them, and boy am I glad that when PJ and New Line had their disagreements, PJ didn't just say, "Well, that's not the story I want to tell" and walk off the project. Raimi had no love for Venom but the producers talked him into it, and Spider-Man 3 will not likely be any worse for that bit of "studio tampering."
I admire an artist with integrity and purity of vision, but if you can't make adjustments and roll with the punches then you are ultimately being selfish and denying the audience the opportunity to see your work. I would have preferred a Wonder Woman that was 80% his vision and 20% studio input, guided and shepherded and shaped by his hand and imagination. Now Joss will keep the 100% version in his head and there it shall stay. But you are not a great storyteller until your story is out there for an audience to experience, and sometimes you have to allow your vision to flex and change. Spielberg and Lucas were completely frustrated with how Jaws and Star Wars were not going to reflect the vision they had in their heads, but they allowed a basically compromised version of their idealized films to be released in theaters. And boy am I glad they did! Whedon might have his integrity, but he'll have no movie (and therefore no audience) if he isn't willing to guide his vision through the expected growing pains and adjustments.
Now, it is entirely likely that the studio heads were giving him demands like, "Give Wonder Woman a really cute dancing penguin for a friend. Kids are into penguins these days." There comes a point where an artist becomes a prostitute, and you need to maintain that balance.
It's just a let down to see his name taken off a high profile project. The guy deserves some mainstream success.