#1 is definitely something that should have been fixed this year. The "Allow Man to Score" penalty is the worst, especially if you're a point guard guarding a Chris Paul or a Tony Parker. These are players that will get their points one way or another. Penalizing almost half a grade just for allowing two points in the middle of say the second or third quarter is arguably the biggest injustice of the mode; you can't hold your opponent down forever.
I think the amount we are deducted should vary by context and situation, and that's probably the best approach to take. If I allowed two points because I got caught on a screen and my teammates didn't help defensively, the penalty shouldn't be too severe. If I allowed my man to go right past me for an easy layup, in the final minutes of the fourth quarter, then I wouldn't mind being deducted half a grade. Definitely hoping that gets fixed in 2K14.