At this point, Supernatural has such seniority and stable ratings that I doubt the network is micromanaging it at all. They have so many other problem series to worry about in the schedule, and I would be very surprised if the network asked Carver for more than a broad outline, and was okay with anything as long as he didn't kill off the leads permanently and there was enough room to go to season 10.
Never underestimate network bosses ability and desire to micromanage. Many not only see themselves as business visionaries, but creative ones. I'm not saying you're wrong, but there's also the flip side: this is one of their best performing shows, so they're invested in seeing it continue to succeed so they can take the money SPN makes and throw it at the struggling shows--usually for marketing.
This is what I wonder. For the network, making money is the bottom line, so did someone say "Jensen and Jared must appear together in 85%'of the scenes" or "flashbacks would be better than having them seperated for four episodes so lets go with that".
I just wonder how much autonomy a showrunner really has with their storylines and how these decisions are made.
Depends on the showrunner and his/her track record. SPN has had three showrunners. If you look at the show as a whole, there's a "brand stability" going on that really isn't impacted that much by each showrunner. IOW, while Kripke came up with SPN and exec produced for five seasons, after he left it was still a CW-type of show and didn't veer too far from what it had become by S3. While huge changes in a show are never a good thing, each showrunner should put their own individual stamp on their seasons--unless they're not able to, either because of their own lack of creativity or because they have to be lock-step with what the network dictates.
It's pretty much Writing 101 that flashbacks are massive failures, in print and onscreen, unless you're doing something totally new, crazy, and different with a flashback--like the whole season is one big flashback or the flashbacks aren't really flashbacks, just written so the audience thinks they are, etc. (and that's not even new or crazy). But choosing flashback over real time storytelling is a bad idea, since its awkward to transition to and takes the viewer out of the moment. How many times did the action grind to a halt when Sam's flashbacks occurred? Dean's were a little different since they were action flashbacks, but still--never a good choice.
From a storytelling standpoint, it would have been better to spend the season with Dean fighting his way through purgatory while Sam searched for Dean, each of them encountering new conflicts and monsters and problems, etc. If Sam had to drag Amelia and Kevin with him and Dean had Cas and Benny, fine. But that would have separated Sam and Dean, and those two being all up in each other 24/7 365 is core to this series, so yeah, I wouldn't be surprised if that was network determined. It would also have required ditching the MOW eps and delaying the mytharc--again, core to the series.
If ain't broke don't fix it--the business mantra. SPN is still pulling in ratings and money, so just keep on keeping on with the same thing. How visionary of them.