This is certainly some interesting news although it does not effect anything when it comes to how Marvel Studios is producing their Phase 3 of films. So don't even start thinking in that direction.
In a new report by The Hollywood Reporter, Marvel Studios president Kevin Feige has maneuvered the studio away from reporting to Marvel Entertainment CEO Ike Perlmutter and will now report directly to Disney Studios chief Alan Horn.
THR received the following statement from a Disney spokesperson:
"Marvel Studios is taking the next logical step in its integration with The Walt Disney Studios, joining Pixar and Lucasfilm in centralizing many of its film-related functions in Burbank, with Marvel Studios president Kevin Feige and co-president Louis D’Esposito continuing to lead the Marvel Studios team reporting to Walt Disney Studios Chairman Alan Horn."
Perlmutter is a rare breed of CEO who is a recluse and is allegedly difficult to work with due to his micromanagement tactics. He may not oversee Feige and Marvel Studios anymore but it's also reported he will still have Marvel TV head Jeph Loeb reporting to him and the publishing side of things will continue business as usual under Perlmutter.
Marvel Studios is on a legendary run of successful big budget tentpole franchise films. With Walt Disney Company owning them and other big moneymaking studios like Pixar Animation and Lucasfilm, having all their studios directly under the supervision of Disney Studios is just smart business.