I agree about the 4-2-3-1 being out best formation, I'd have that every week, but our defence was generally stretched because of the shite served up in front of them. Our back three has also had some really good games against Frankfurt twice, the Huns twice and others. Those games we performed well in always had two sitting in midfield. If we'd gone 4-1-4-1 today, as I had thought we might be when I saw the team, I think we would have really struggled. The common denominator in our poor performances seems to be playing Clarkson deep and Shinnie further up field. It's certainly worth looking out for, as I have a strong suspicion that if Barron leaves this window, we'll see Robson return to having Clarkson deep (even in a four: 4-1-4-1) and we'll start to fail again.
The reason it bothers me so much, and it's nothing to do with anything you've written, is that I've seen (on forums) and heard at pittodrie people questioning our captain and saying "his legs have gone" (the world's most irritating cliché), or "he's done" (often suffixed, ridiculously, with "at this level", as if we're at the pinnacle of the game). It simply isn't the case. His best games this season have all come from playing in a two. Shinnie needs to be facing the play so that he can drive with the ball and nip at folks heels from goal side. Not having a defender clear the ball over his head and have to chase it back, or to play high up the park and receive it to feet just outside their box facing backwards. What we were witnessing was a player doing the work of two players and being run into the ground doing so. The technical side of his game is no worse than it was in his first spell, he's not quick to spot a pass and often makes a poor decision when a more lucrative pass is on. Most fans (certainly around me) don't seem to get the nuance in formation and position, they just see a guy chasing the ball and criticise. That shitey midfield setup has not only wrecked our league season, but also had a huge detrimental effect on the fans views of our captain. Hopefully the next time Robson tries his shite, more folk will side with Shinnie and not the manager, but I don't hold out much hope.