I think that's true on both sides. It is both true that most studios mess with their artists' work. It's also true that this affects quality negatively, generally. This is still true at Marvel studios. Pointing out that the movies still do well and are successful doesn't address this. After all, whose to say that the movie wouldn't do even better without their meddling? I certainly would've enjoyed a Thanos-less GotG or a Cave-full AoU more. I think we all would have enjoyed a SHIELD-less IM2 more. Even to say that they have a checklist and nothing more (item 3: don't have farm scenes?), doesn't negate the idea that that checklist, or perhaps the inflexibility of it, takes quality away from films for the sake of connecting it to the larger story of the MCU. You reducing the reality of the executive-mandated weaknesses of this movie to "Executives are evil and the MCU is ruined!" is just as much a strawman as reducing your point, that the MCU is successful despite, or perhaps because of it's quality-reducing meddling to "artists don't matter."
Now, some directors are fine. Gunn is a great example of someone who takes Marvel Studios making his movie worse and shrugs and continues on. That's the kind of attitude you need as a director, to work with Marvel. They're going to come in, ask you do make a poor decision for your story, and not take no for an answer. Moreso than other studios, judging by how many take umbridge with MS and not any other studio. Without knowing how badly they're going to gut your movie, it's impossible to know beforehand if you can handle that. Wright didn't know for nearly ten years that Marvel Studios were going to make him make the change that (in his opinion) weakened/gutted his film. It's possible those who've had good relationships so far, like the Russos had decisions that really didn't hurt the film. Cutting out Arnim Zola walking didn't actually hurt Cap 2, it helped it really. This may not be true in the future, as we've seen with Whedon. After all, being told to cut Wasp didn't hurt Avengers one bit either, actually made it stronger. The rarity of return directors and the increasing use of newcomers are further indicators that being a director for Marvel Studios is especially difficult.
A better counter would be pointing out how those weaknesses and meddling are necessary to connect the universe and make everything more successful overall, even if it does sometimes lower the quality. A less credible point might be that their changes make things better just as often as worse and we just don't know. Or you could just go crazy and say you liked all the SHIELD in IM2, or Thanos making Ronan cooler, or Malkeith being underdeveloped made him more mysterious, or some other outlandish minority opinion, and stick to it. Or you could just continue the ad hominem attacks. Whatever. It's your world.
Throw the baby out with the bathwater? If you love something, you don't just walk away because someone makes a mistake. You tell them to correct the mistake. It's only after they've proven that they don't give a crap about the quality of it that you stop supporting them.
