1st and foremost - I am a veteran of this series and a huge fan. excuse me if some of these issues have been addressed in the latest patch. I'm running 4.09

1: HUGE issue - QB's Calling their own number too much on RB designed plays and fumbling the ball - Infuriating - I understand the QB fumbling at a higher rate when they get sacked, I get that. But for the love of god, If I call a play for a RB it should go to a RB

2: QB Scrambling looks great! Sometimes - However, the QB needs to make a sideline run for the first down marker more often and get out of bounds, especially if they are not a running QB. also when the QB is throwing the ball away they should be rolling out of the pocket 1st otherwise it's a penalty
---- a side note: when the QB Scrambles then throws on the 2d screen it sometimes looks as if they pass the line of scrimmage and if the pass is complete they give credit to the QB for a run AND yardage for the pass. The play recap will say [QB x Scrambles for 30 yards] when it shows on the 2d that they at the last second passed the ball. double yardage

3: Custom Passing Plays the offensive line does not block and the QB gets wrecked.
---needs to be a roll out logic for the QB - Drop-back options would be short, med, long, rollout Left or Right

4. I'd like to see declining penalties strategy post snap. Example: If Im on defense and have a team 3rd and long on their side of the field and the result of the play isn't a 1st down and they get a holding call, I'd decline the penalty and force them to 4th down. there are some situation when you want to decline penalties when you're on offense as well

5. Free Agency is a mess - The AI should be signing top talent like crazy but I often have overall 90+'s unsigned going into week 1. Players should be accepting whatever the highest offer they have on the last day of bidding for free agency.
--- The A.I. should also be snatching up as many players as it can when they have a practice squad

6. A.I. cutting players for cap space needs to be looked at as well. They often cut the best player on the team. Maybe create a no cut list of the top 5-10 overall players per team then the A.I. can cut anyone under that to make cap room

7. there needs to be a WR4 position on the depth Chart

8. Needs to be a hail Mary play (could be handled at the custom play creator, if the O-line would block)

9. Holdouts!! Franchise Tags should piss players off (lower Morale) especially if they've been franchised previously. Players on contract that make pro-bowls should be looking for extensions the next year or the will hold out

10. PED suspensions - on field fight ejections and suspensions

11. Players that don't play need to regress and/or Retire

11. Firing staff during the season for player and A.I. - Staff Friction where one member says "it's me or him"

Have only had the game a few days officially.the 7 day trial I spent almost entirely experimenting to see if I would like the game, purchased 2 days now and actually "getting into it"
I have not played a season yet..week 1 lol..so hope that by my finish , there may be a fix to the AI free agency thing you mention. The only one of your points that I have seen directly has been the penalty decline type issue, which annoyed me lol.
I have made a few custom deep throws that work very well...almost too well if they were an opponent lol... 4 wideout bombs that are averaging about 55% hits in total, about 10% to the short dump off back running underneath, and the other 45% to one of the deep route WRs, nearly always 40yds+... so sometimes the line does block.
I agree with nearly all of your points though, those last few suggestions would be great.

Enjoying the game, just feedback I've had.

- Re-signing players is a chore. You have to go to each individual player's screen, place an offer, and then wait a week for them to decide (not a problem). However once they've decided, the previous contract you offered isn't saved (so you need to write down your last offer or remember) AND you have to go all the way back around into the player card again to offer a contract. There needs to be a shortcut. I legit have half of my team coming up on free agency, and I'm going to let half of them walk because re-signing them is a bore. EDIT: Players should be adjusted to automatically accept the offer if you meet their wishes though - I'll meet wishes just to avoid the negotation back and forth...but then the player comes back and says the financial side needs more work.

- I don't like how we get less functionality in Sandbox mode. Why can't I use a "watch list" in Sandbox Mode? I also wish I could use the trade block.

- There is no easy way to easily look at each team's roster (at least in Sandbox mode). If I want to see which team has a weak RB core, how can I do that easily? Currently, the only way is to manually click on to each team, then go to their roster, but when you click on the team it takes you to their home page first, not the roster. Back up to the re-signing players, it just seems like there's a lot of extra clicking and drop down menus (I could be missing something). LATER EDIT: For anyone reading this, going into "search" and choosing the desired position and sorting by team does an okay job of presenting everything on one page

- Bookmarking pages like the OOTP series