Ok Paul, I will get to you tomorrow lol.
Dave, your defense is ...... f###y I'm going to assume that the DL playing one of your 3 safety spots wasn't exactly intended. Starting from the line of scrimmage, I am guessing that on anything other than an immediate handoff your strong side DL is so wide, he is being put into "coverage mode". Your two interior LB are close enough to the LoS, that they are on an auto rush (saw this in another match- opponent as running a true 4-3 but the OLB were tight to the line and that put them blitzing more often than not). Your weak side DE probably acts like you want (maybe because of the safety in position closer to the sideline. Just a guess, but I think your strong side DE will need to be inside the TE or you would need to stack someone a little closer to him but deeper.
The secondary seems to gravitate to the receiver that runs to their zone. And yea, there is potential pitfalls on this. If you go to game 1, on the play just before your second score (pause and go slo-mo, I couldn't block you due to skill differences), this is a designed pass play with a 2 second delay. Your strong DEthinks himself a LB and due to his position on the field, he drops into coverage. Watch that play a few times and look at who all ends up covering the TE, look at the receiver on that side about to come open, and look at both RB's. The one going right I don't believe is covered, and the one going left I think gets uncovered if the play lasts a half second longer, because that safety looks to be blitzing. Why, I don't know. I have seen MLB's act the same way.
What I can't explain -
If you go to my scoring drive at the end of the game, I ran the same play back to back, but there were different reactions by some of your defenders. 4th quarter, 9minutes in. First play my QB runs forward, everything derps. Next two plays actually run as intended. The play has a delay, and before the QB gets rid of the ball, you defense drops into coverage and your secondary starts to look for people running down field. Your DL "safety"appears to take the play side back and eventually run by the ball carrier. Your S 2nd from the top latches onto the WR running deep as there are no other receivers in the vicinity and the afore mentioned DL was already covering that RB (why, no clue). The TE and other WR draw the attention of your othercondary players, and this leaves the other RB to make a play. The very next play (exact same play call), that 2nd from the top safety decided to blitz, leaving your DL "safety" to take on the role vacated by the blitz and go double that WR. I am pretty sure that the play side RB is not covered and very much open leaving him free to block for the other RB. I have no idea why there wa a change in the defensive coverage on this play, in comparison to the play before. I blame RNG at this point.
Best guess in a short synopsis, your defense is too unconventional and the game format cannot fit your positioning into its parameters. As that defensive formation would never be used against a base offense (12 personnel) in a real life situation, I agree with the game - it shouldn't work.
All that with a grain of salt tho, as I am fairly certain your kicker could have played RB and you would have dominated me. Really hard to get a full grasp of what is happening when everything falls apart so quickly!