A lot has happened in the Marvel Cinematic Universe since Joss Whedon last directed a film there, but he still thinks Marvel is a brilliant place to work. Specifically, he thinks that Marvel's brilliance comes from the studios' willingness to take directors who might not be the first choice anybody would make for a major tentpole release, and let them not only direct the films but be given a voice in their creation and direction. Speaking during a roundtable of several Marvel directors that is included in the digital release of Avengers: Infinity War, Whedon said...
Something Marvel does that is brilliant and it applies to all of us is that, nobody here necessarily had the resume to make the next big action film. They were interested in having that person speak they weren't interested in saying, 'look just do, just hit the marks.' They wanted each one of us to bring ourselves to the movie and you can tell, as much as there's a throughline in Marvel, you can definitely tell who's who and what they constantly want to talk about.
While many have always assumed that the larger continuous story of the Marvel Cinematic Universe has always taken precedence over each individual movie, Joss Whedon, and the other directors involved in the roundtable, who include the Russo Brothers, Peyton Reed, Ryan Coogler, Jon Favreau, Taika Waititi, and James Gunn, insist that it's not really the case. Rather, as Whedon says here, each director was not only allowed, but expected, to use their own voice and creativity. James Gunn mentions that he was never asked to have Guardians of the Galaxy Vol. 2 end in any particular way for any particular character, simply that he gave the Russo Brothers an early copy of the script so that they would know where the characters were while incorporating them into Avengers: Infinity War.
It's difficult to argue that Marvel doesn't let its directors do their thing when you look at a movie like Thor: Ragnarok which was something quite unique compared to previous Thor movies. James Gunn's voice helped create the Guardians of the Galaxy, so much so that nobody is quite sure what's going to happen to them now that he is no longer involved. None of these names were exactly household ones either, showing that Marvel was willing to take a chance on the people they believed were ultimately right.
What's next for the MCU is anybody's guess. With Phase Three almost over and significant changes to Phase Four quite likely, there will, very soon, be a whole new crop of directors ready to lend their own particular voice to the Marvel universe.