Marvel Entertainment is not Marvel Studios, thank goodness.
Once upon a time Marvel Studios (movies), run by Kevin Feige, was under Marvel Entertainment (comics and TV), run by Ike Perlmutter. It's no secret that Feige and Perlmutter clashed heads over creative control of the movies that were coming out. It all came to a head, it seems, with the production of Captain America 3 where the Russos made the case that they would have to do Civil War which would involve getting RDJ who is not contractually obliged to make this film. Feige was creatively on the same page as the Russos but Ike, who is notoriously frugal, absolutely didn't want to spend the millions to get RDJ. In the end Marvel Studios was pulled out from under Marvel Entertainment and Feige now answered directly to Disney. Some folks posited this shakeup in Disney was a sign of impending doom and tried to portray Feige as a creative bully dissolving the creative council of Marvel Entertainment. In truth, it seems, Ike Perlmutter, was getting in the way of Marvel Studios and this was the best way to handle it.
So, Stark is out as Iron Man? That's all on Marvel Entertainment. Blame Ike.
Captain America as a HYDRA agent? That's all on Marvel Entertainment. Blame Ike.
Female Thor? That's all on Marvel Entertainment. Blame Ike.
I think Marvel Studios, under Feige, without Ike's input, is only going to give us better movies.