I think I called it flaws, not weaknesses. Mainly, I saw problems with the roles the midfielders have to play in that particular set-up and how to get the fullbacks involved in the game.
I agree with this and I never said anything different. Your post is slightly confusing, you use so many different examples, but I try to answer. Let me know if I misunderstood something or didn't answer the question you were asking
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First of all, I don't really understand your comparisons to Barca's midfield in recent years (or Bayern's at the moment). The key defensive concept in these teams was a high defensive line with pressing as a huge team effort. It was about controling the space and demanded a fair share of defensive work from every single player. It doesn't matter if Deco/Scholes individually offer more defensively than Xavi/Iniesta if they have different roles to play in defense.
Maybe there's a bit of a problem with the (or my) definition of counter-attacking football. Quick transitions after forcing the opponent to loose the ball is a very active way of defending and attacking. In my opinion, counter-attacking describes soaking up pressure to force the opponent to commit more players in attack, which opens up gaps in his defense that you can exploit. It's a reactive strategy. Of course teams often can do both, but usually one is the plan, the other happens incidentally.
Neither has necessarily to do with dominating possession though. I really hate Guardiola's Barca for putting so much focus on those meaningless possession stats. Teams can control the pace of the game with and without the ball, play wonderful technical football with 40% possession and boring football with 60%. A team is successful when possession has a purpose and can be used efficiently.
Last season we were an exeptional counter-attacking team, this season not so much. We're still great in transition, but we rarely play a game like for example last season against Barca.
I hope that answers your question(s)?