I honestly think that there are a couple of things that we could do to at least not look like the entire team is lost.
1. STOP with the RPO. The decision to Run or Pass is happening behind the O-line, so they have no idea what technique to use, so they just don't use any... If they are going to simulate an RPO, then predetermine if it is going to be run or pass and an audible simply means it is changed from pass to run or vice versa. Let the O-line fire off the ball and hit someone, this line is capable of playing smashmouth football, but not if they are being asked to adjust what technique to use after the ball is snapped. It's a frigin mindset, and if you are uncertain then the Opposing Defense has the advantage.
2. Take snaps from under center. I think it was the guy that does the "tape never lies" that pointed out that Trubisky seems to have better footwork when he drops back from center to throw. It might be a feel thing for him, so give him what feels good. Another advantage about being under center is that the RB has momentum moving FORWARD. In the RPO both the QB and RB standing flat footed reading the defense and from the pistol or shotgun formations there is no momentum, just a stupid shuffle. Additionally, it seems that the play action pass is a little easier to sell.
3. If you are going to throw the ball deep with Trubisky (and I do think that they need to call some plays where that is the only play), then try to make sure it is in the middle of the field. He simply can not throw very well along the sidelines where he needs to drop it over a defender.
4. Roll him out of the pocket, he has gotten the deer in the headlight look, and I know he is recovering, but I think to get some feel for running again they need to roll him out to the longer side of the field and let him throw on the run or tuck it away. BTW, I am not talking about a naked bootleg (too cute), play action followed by some protection, if they are capable of that.