As much as I like Kelly and believe he's the right man for the job in the long run (12-1 last season, not a bad record at all) after seeing this game I believe it emphasizes what I see as a typical Kelly type of offense. Typical in that he relies upon the one QB who has no real ability to move and really cannot throw well or can be relied upon to throw well in difficult situations. This stubbornness has been seen since his arrival at ND (Tulsa). (meaning he relies upon TR to be something he's not - a thrower)
Cam McDaniel runs well so, it must be GAIII's turn to run the ball. Theo Riddick is gone but fleet-footed and light RB Carlisle is Theo incarnate if you watch the UM game - where clearly he's not Riddick (at least not yet and likely never will be - look up injury prone). Just bad decisions made on his personnel. Fitting a round peg in a square hole. He did this to Riddick making him a slot man. Good athlete, not a great idea. Carlisle, very good athlete and good slot man, but mister pound it up the middle RB, maybe not a great idea.
He has Troy Niklas - the clearest mismatch offensive mismatch on the field - sparingly used (I can't think but one play in the first half where he was used.)
These are just examples not good game plan coaching.
Take Hoke's coaching - Gallon (sp) and Gardner were complete mismatches for ND and he abused ND with them, beginning to end.
I guess what I'm saying is, this isn't Grand Valley where coaching a player giving him some technique can turn an average player into an effective player regardless of position. He's now in a league where you teach technique to turn very good players at a position into great players at a position, not turn them into good players who fit and idea and hope they pan out. (with that said, some players don't know where their best or natural position is ie. Niklas, Russell and now Carlisle. We see Carlisle might very well be a slot receiver where Riddick really wasn't.)
Back to Tommy. He's not a great QB so stop trying to make him into one. He's the only QB at ND (seeing Hendrix isn't going to get a shot at it - Kelly sees him for what he is;) so treat Rees like the QB he really is. Get a running game with RB's who can do the job of running it - Cam McDaniel and get the other three (Mahone, Folston and Bryant) up to speed quick as you can. In other words, ND needs to be a running team first with Passing second on the list.