I don't think there's a formation that we could use that would solve our left side problem. We don't have a full back worthy of the name to play on that side and we're lacking a winger as well. Maybe Shinnie on the left of a four would be alright, be he wouldn't have much ahead of him so we'd still be pretty shite on that side. As @RicoS321 says, that's a squad-building issue. Likewise in the middle of the park, we just don't have the player(s) that we need to win the battle and control the game in there.
If Jimmy is responsible for that then it's a big worry, if he isn't then it's also a concern but perhaps one that has been addressed with Lutz's arrival. He said in his arrival interview that there are one or two positions we need to sort out and I'll be amazed if it isn't left back/left wing back and centre mid. If we're not blaming Jimmy for recruitment then I'm ok with him getting until the end of the season but it'll mean Lutz has a hell of a lot of work to do in January.