I absolutely agree with you on the fact that they didn't entirely fix the damage CW did to Reed's character. I think with the Negative Zone prison it was highly implied in Hickman's run that it had been closed given Johnny's prolonged stay while being presumed dead. As for the Bill Foster death, yeah...given that the character will be showing up in the new "Ant Man and the Wasp" film this year, I would be really surprised if it wasn't undone at some point in the near future.
That unfortunately seems to be the best solution to bad plotlines or mis-characterizations - the future writers simply ignore them as if the stories never happened.
I think the embargo on the FF is technically over, although given what i consider to be a sharp downward trend in quality of Zdarsky's MTIO "Fate of the Four" story, I'm hoping that they wait to give a renewed Fantastic Four title to a better writer.