Who's to say that this hasn't been in the plans all along? I man were talking about Marvel here, the company that has set up a years long storyline with characters. I don't think they've just been winging the show, it's all a part of the plan from the beginning.
But now that these things are starting to come to light people are jumping to "oh they knew they screwed up and now they've fixed it" scenarios. When in reality all signs point to this is how it's been planned all along.
It's still very much the same show they originally pitched; normal shield agents going against superhuman and other world threats. Nothing has changed the show is just progressing as its been planned to.
All this news is fantastic, I can't wait for the rest of this season and the multiple seasons beyond!!