IMO a lot of what you mentioned is a talent issue not a coaching issue. Hard to shuffle the lines when the team is made up of centers and centers who can't play other positions. Having a mucker on every line is pretty standard in the NHL. When the entire d-corp is made up of one way players who can either defend or move the puck and not both, it doesn't really leave many options. As far accountability, the prized UFA signing was benched to the 4th line and Hartnell is no longer on the team. I think that's pretty good start.
Depending on how you the view the roster, Berube deserves the benefit of the doubt. I think the roster is mediocre at best made up of high end role players. Giroux and Voracek are the only top 6 forwards on the team as of today and Coburn is the only top 4 defender IMO: doesn't leave a lot to work with so getting in the playoffs was an accomplishment.
That's true, the roster doesn't leave him much to work with. But there was the whole Mez/Gus fiasco and after Mez was moved and Grossmann was slumping, and he still wouldn't play Gus, it shows that Berube is choosing the guys that can only play one-way over a guy like Gus who can play both ways.
Berube may have been a part of getting Hartnell moved, but in the end it was Hextall's move and we never saw any accountability for his poor play or penalties during the season. Vinny is the only guy that saw his ice time affected by his actual play while there were many guys who were deserving of less ice time at different points during the season. Berube talked about accountability, but really didn't deliver.
Other than that, I think you're selling our forwards short. Simmonds, Schenn, Hartnell and Read could all be considered top 6 guys as well. Voracek is probably capable of driving his own line possession and playmaking wise, but we never got a chance to see it. Read has a great shot and offensive instincts, but he was stuck in a defensive role the entire season. Simmonds and Vinny on the same line was stupid because they're both poor defensively and neither are good with the puck.
There were just so many things he could have done differently with the forward corps and he never tried anything different. The 2nd and 4th lines were complete liabilities the entire season, while we never got to see Read in an offensive role or tried to break up our two play makers/possession players in G and Voracek to spread the offense around and balance the lines.
We were completely reliant on the top line producing when they didn't have any reliable goal scorers with Hartnell's poor year. When they had dry stretches, the team lost. When our top line got focused on in the playoffs, we lost.