I think the 49ers game was a turning point. 1) Without Byron Jones the communication issues were abundant. 2) Now that both Howard and Jones are getting healthier. Flores can implement his vision he had for the Defense when they signed Jones. 3) The ability of the CB's to shutdown opposing WR's has opened up the blitz packages and stunts along the line. The multiple fronts and disguised looks gets amplified with great secondary coverage. 4) Miami has arguably 2 of the top 10 CB's in the NFL, most team can't say that. This is a huge advantage for Miami.
If both Jones and Howard can stay healthy this is going to be a very hard team to beat, moving forward.
Let's hope they can learn how to stop the run. Once they do it consistently, I'd think it be the point they've progressed into a top echelon type team.