I think this one's been mentioned already, but just in case.

NE got 2 points via penalty here but the penalty should have been half distance to goal. I guess the choice should have been

2nd & 20 from the 4 if Accepted
3rd & 16 from the 8 if Declined

1:42 1st and 10 Cin - 14 Rush by Burrow, J. for -6 yds. Tackle by Winovich, C.. CIN 0 - NE 7
1:33 2nd and 16 Cin - 8 Rush by Burrow, J. for 0 yds. Tackle by Winovich, C..
Cincinnati Penalty on Higgins, T.: Unnecessary Roughness.
The play results in a SAFETY! CIN 0 - NE 9

Just thought of this and I'm going to toss it out.

There's 2 types of basic penalty.
1) Occurred during the play. Accepting one of these usually cancels the previous play.
2) After the play. These are the Personal Fouls and probably the Unnecessary Roughness penalty above and misc others. These are normally always accepted and yardage from the previous play stands.

A lot of players have been saying that the current system where we get asked if we want to accept a penalty or not before we even see the play is awkward.

Why not automatically accept the 2nd type of penalty? All the personal fouls. Don't ask the user. Show the play normally and after it's over blow a ref's whistle and tell the user about the personal foul and apply the yardage. This gets rid of the awkwardness for a fairly large percentage of the penalties that are called.

For the others, how about giving the user 2 buttons that show clearly the result (down, yardage and field position) of accepting/declining the penalty directly on the buttons? I know the rules fairly well, but I'm pretty sure I've goofed a couple of times and made a selection that was disadvantageous to me with the way it is now.

Be careful with this one. There are many personal fouls and unnecessary roughness calls made during a play.

Correct, but at the moment it looks like they are all "after the play".

As far as I can tell, from watching games closely:

I think you get the penalty yardage regardless of how you answer the Accept/Decline question.
And the play result is never cancelled.

Fixed a bug for the next patch.