My take:
Alan Taylor - I get why he's upset. I will say this guy has been the classiest on how he responded to the media when this stuff was brought up. I give him full credit for that. On the downside, while I liked the look of Thor 2 better, Branagh did a better job directing the actors.
Ed Norton - Ed Norton the only one of the MCU actors to sign a one picture deal, and he didn't want to do TIH in the first place, he initially turned down the role. I could care less about his beef, because when you sign a one picture deal, you're not interested in the future of the character.
Hugo Weaving - Not sure about this one. I'd heard he hates big budget movies, He refused to do another Transformers as well. Other than working on the Wachowski's on Cloud Atlas, (for understandable reasons, they turned him into a superstar) he has never appeared in another big budget film since CA:TFA.
Avi Arad - I don't want to be too hard on this guy. He did pull Marvel out from the pit of bankruptcy, and made them profitable. However the guy was the CEO of a toy company and knew nothing about the movie industry. He far more interfered with the Marvel films than Feige has. It was Avi's fault that Terrance Howard was hired in the first place, and didn't help matters when Terrance threw a hissy fit when he didn't get a raise. He signed some horrible deals with the other studios. Yes they were trying to get themselves financially solvent, but I think they had more bargaining power to make better deals, even if Marvel Studios never had been created.
Mikey Rourke - I get his beef. No one likes to see their shots on the cutting room floor. However the alternate ending where he kidnaps Pepper was terrible, so I hope there was more to it than that. The guy is a tremendous actor and yet a total nut job. This is the guy who quit acting to take up a failed boxing career that messed up his face and resulted in numerous plastic surgeries that make him look like Frankenstein's monster. The reality is he's been receiving less and less work, so whatever his beef was for his public lambasting wasn't very smart for his career.
Patty Jenkins - cry me a river. This is a business. You were hired to direct a comic book film. You should know going in that no one is going to give you total creative control. No harm no foul. No one cares that she was fired. She's a great director, but she shouldn't have taken the job.
Terrance Howard - the architecht of his own demise. I bet Don Cheadle got paid over a million dollars for a few days on set for Age of Ultron. That could have been Terrance Howard. Sorry buddy but no one went to see Iron Man because of you, and I thought you did a great job in that film. You should have known how uncomfortable it was the fact that Favreau didn't want you, but was forced to take you because of Avi Arad.
Natalie Portman - this one makes me the most sad. I know alot of people have bad reactions to Jane, but I like her character. However as I said with Jenkens, this is a buisness, and Portman knows that too. I get her loyalty and upset that she was denied the opportunity to work with a friend. However I call BS on the article about her not wanting to appear in AoU. There is no evidence that they wanted anyone other than Hayley Atwell, Idris Irba, and Tom Hiddleston to play cameos from the other films.
Edgar Wright - I dont' have a side on this one, it's just sad that it didn't work out. However Edgar should have been realistic when the MCU started taking shape that his work would have to fit into that world. Do I blame him? No, but I think the vitriol from some of his fans has been beyond stupid and it's unfair to take that out on Peyton Reed.
Joss Whedon - probably the most overblown of all the situations. Sure there were frustrations, but in going back and listening to his interviews, most of what he said was taken out of context. In the end he said "this is the cut that I wanted". Pretty much end of story for me.