I think Penn can be a talented guy when his hands aren't bound by a studio. Anyone who's seen The Grand and Incident at Loch Ness can attest to that....I think. Granted both of those films had a bit of improvising and weren't placing any scriptly demands on him...
Still, Marvel's been good about letting the directors of The Avengers series let loose. I don't trust Penn entirely, but I do trust Marvel. Hell, they let Norton take a crack at his Hulk script just because he wanted to. Same with Downey Jr bringing in Justin Theroux on IM2. They trust their cast and crew to use their best judgment and it's paid off pretty well. I was surprised to find out Penn had even written Hulk considering how much I liked it.
I never thought I'd defend this guy, but all of Penn's laughable Marvel films have been under Fox's thumb who are known for their mindless frugality. I don't know what kind of film was hidden under X3 or FF or even Elektra, but Fox likely had a gun to his head. He might be sacrificing his integrity to please the studios but I believe Marvel are good at nudging creativity and openness from their people.