This is purely anecdotal, but I see more passes for negative yards than I would expect. I realize that screens and swings can lose yardage, so it may not be a problem, but it just seems like it happens more frequently than I would think. Same with runs, though it's not as obvious.

One thing I've been noticing for a while is that spikes seem to be used before time outs in many situations, and I think timeouts would be used first. Here's an example:

Dallas is leading 6-0 and there are three minutes left in the half. They have three time outs. But driving with 3:12 left, they spike the ball on first down. I think in real life you'd use the first time out here instead of spiking.

You may have more advanced logic, but it seems to me like you'd do something like this:

If you have 2 or 3 timeouts and and there's more than 2 minutes left, you call a timeout.

If you have 2 timeouts and there's more than 1 minute left, you call a timeout.

If you have 1 timeout, you don't use it unless you're in the last minute and can't spike it.

Dallas
2nd Q 4:30 1st and 10 Dallas 30 free agent scrambles for 10 yards.
2nd Q 3:48 2nd and inches Dallas 40 free agent (pressured) passes complete to Dustin Keller for a gain of -4 yards.
2nd Q 3:26 3rd and 4 Dallas 36 free agent passes complete to Lee Evans for a gain of 8 yards.
2nd Q 3:12 1st and 10 Dallas 44 free agent spikes the ball to kill the clock.
2nd Q 3:10 2nd and 10 Dallas 44 free agent (pressured) passes incomplete to Dustin Keller. PENALTY. Neutral Zone Infraction on Kevin Williams. 5 yards.
2nd Q 3:02 2nd and 5 Dallas 49 free agent passes complete to Steve Breaston for a gain of 34 yards.
2nd Q 2:17 1st and 10 Duluth 17 Brandon Jacobs rushes for -4 yards. Fumble, recovered by Dallas Two minute warning.
2nd Q 2:00 2nd and 14 Duluth 21 free agent passes incomplete to Jerome Simpson.
2nd Q 1:53 3rd and 14 Duluth 21 free agent passes incomplete to Steve Breaston.
2nd Q 1:46 4th and 14 Duluth 21 Stephen Gostkowski field goal attempt from 38 yards. Good.
Dallas 9, Duluth 0

In this situation, I think I'd punt it. It's a hard first down and the opponent needed little progress to make an end-of-half field goal. Perhaps the rule would be that if you're in your own territory at the end of the first half and it's fourth down, you punt (unless you're Fat Elvis).

Duluth
2nd Q 1:41 Duluth -1 Stephen Gostkowski kicks 70 yards. No return. Touchback
2nd Q 1:33 1st and 10 Duluth 20 Philip Rivers passes complete to Hakeem Nicks for a gain of 9 yards.
2nd Q 0:48 2nd and 1 Duluth 29 Philip Rivers passes incomplete, dropped by DeSean Jackson.
2nd Q 0:41 3rd and 1 Duluth 29 Rashard Mendenhall rushes for -1 yards. time out Dallas
2nd Q 0:33 4th and 2 Duluth 28 Philip Rivers passes incomplete to Greg Olsen.
Dallas 9, Duluth 0

Dallas
2nd Q 0:23 1st and 10 Duluth 28 free agent (pressured) passes incomplete to Lee Evans.
2nd Q 0:15 2nd and 10 Duluth 28 free agent (pressured) passes complete to Jerome Simpson for a gain of 10 yards. time out Dallas
2nd Q 0:07 3rd and inches Duluth 18 Stephen Gostkowski field goal attempt from 35 yards. Good.
Dallas 12, Duluth 0

Oh, and you may have built this in already and it was just a random draw, but I noticed in one of my Week 13 games that my kicker made 4 FGs of 50+ yards. That's great, but if the random draw is based on just his kicking percentage, and if he went 1 for 1 at 50+, it might make him a little too strong and it might be somehow possible to game the system on that. (I'm not sure how, but if it's possible, someone will do it.)

Would you take the kicker's real-life percentage and put a random variation around it? Or perhaps cap a FG percentage at 97% or something?

This is a very low-priority wish list item, in a situation like this where it's obviously the last play of the half, a hail mary is often in order. I don't care, but a future customer might fire off an angry e-mail if they see a pass for -1 yards. Can we override in that situation and make it incomplete if it's less than a 5 yard completion? I wince when I saw that because it might not be a good solution, but I'm not sure how else to address it.

Not a big deal either way.

(Edit: this was a 4th down with a few seconds left in the half. I forgot to paste the play by play and don't remember the game now.)

The same kicker made two more 50+ yard kicks this week.

Another situation where I would probably punt it if there was a chance that the other team could pull off a play. However, with 6 seconds left it may have been the smart play to just run the ball. Depending on how you do the timing and clock countdown, this may not be a problem.

Austin
2nd Q 1:03 1st and 10 Austin 25 Matt Ryan passes complete to Darrel Young for a gain of 10 yards. time out Austin
2nd Q 0:55 2nd and inches Austin 34 Matt Ryan passes incomplete, dropped by James Jones.
2nd Q 0:48 3rd and inches Austin 34 Mike Tolbert rushes for 0 yards.
2nd Q 0:06 4th and inches Austin 34 Roy Helu rushes for -3 yards. Turned over on downs
Austin 3, High Point 6

In looking at a couple of random games, there were 6 completions for negative yards in the Austin-High Point game, 6 in the Fort Wayne-Clearwater game, 5 in the Springfield-Chula Vista game, 2 in the St. Joseph-Ventura game, and 2 in the Portland-Independence game. Maybe it's not a problem. How common are negative pass completions?

Not a big deal, but if a team kicks a field goal in this situation, the odds are that they ran the clock down before doing it. The other team probably shouldn't be able to run a play.

Independence
2nd Q 0:06 1st and 10 Portland 44 Josh Brown field goal attempt from 61 yards. No good.

Independence 20, Portland 6
Portland
2nd Q 0:01 1st and 10 Independence 49 Jake Locker (pressured) passes complete to Demaryius Thomas for a gain of 10 yards.
Independence 20, Portland 6

Not a big deal, but most teams would likely take a knee in this situation. However, fixing this would create a vulnerability at some point for an error, so probably not worth fixing.

Anchorage
4th Q 2:13 4th and -11 Anchorage 49 Onside kick failed, recovered by the receiving team on Anchorage 49 yardline.
4th Q 2:05 1st and 10 Anchorage 49 Alex D. Smith sacked by Jason Babin for a loss of -6 yards. Two minute warning.
4th Q 1:57 2nd and 16 Anchorage 43 Alex D. Smith passes complete to Nate Burleson for a gain of 21 yards. time out Fort Worth
4th Q 1:49 1st and 10 Fort Worth 36 Jonathan Stewart rushes for 3 yards. time out Fort Worth
4th Q 1:41 2nd and 7 Fort Worth 33 Jonathan Stewart rushes for -5 yards.
4th Q 0:51 3rd and 12 Fort Worth 38 Jonathan Stewart rushes for 3 yards.
4th Q 0:01 4th and 8 Fort Worth 35 David Akers field goal attempt from 52 yards. Good.
Fort Worth 10, Anchorage 55

At the end of my game (Austin) against High Point, I had a chance to kick a game-tying field goal. On third down at the 33 yard line a threw a negative four yard pass. I know that this stuff happens in real life, but it seems that a QB (other than Mitch Crassle) should know its better to just go out of bounds there than risk negative yards.
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Yeah, I was torn on that one. It does happen, but it should be rare.

On the long FGs, I do use a cap in max FG accuracy as a function of distance. So no one is 100% efficient in long FGs, even if they made them all during the season. I'l send you (RM) the caps I used for a sanity check later.

On 4th and negative 11 from the Anchorage 49 with 2:13 left, Fort Worth, down by 42 points, attempted an onside kick that traveled 0 yards that was recovered by the receiving team?
Huh?

Oh, weird. I never even noticed that.