I think their should be more emphasis on the Coaches within the game. At the moment it seems that all people are interested in is who is the Head Coach and what playbook they run.
How can they be more relevant.
1. Each should be able to Scout players in both free agency, trades and draft classes. Rather than have a Universal system for Player Weightings each coach has their own unique weights for each position. This would allow you to get three opinions on a player as well as your own individual weights (or the default set).
A positional coach would give his view on players in his position eg Kickers, QB's, DL etc. An Offense Co-ordinator or Defense Co-ordinator would give views on either all Offense players or all defense players. Finally the Head Coach would have an opinion on every player in the game.
The better rated a Coach is, the more accurate he should be in his assessment and over a period of seasons you would grow to trust the opinions of the better coaches.
It's possible that at draft time they could recommend 3-5 players for the positions they have control over. Whether you choose to accept their views or go with your own would still be down to your own decision.
2. A coaches prefferred style should have an impact on a players happiness and progression. This would allow some players who bust at training camp to go elsewhere and thrive and vice versa - this would be impacted by volatility and each player would have a preferred coaching style as a hidden attribute, some where he would improve but more steadily, some with no real impact and some that would accentuate a bust.
Other teams could then look to gamble on said player who may settle elsewhere and blossom. A player with an obvious bad relationship with a positional coach/co-ordinator or Head Coach could show his dissatisfaction with his status eg Livid, Unhappy, Neutral, happy etc and his 'attitude' could have an impact on team morale.
Might be an idea to give a Coach some sort of 'Personality' eg Upbeat and positive (Pete Carroll) through to Dour and Meticulous (Bill Belichick) with a players volatility, intelligence and discipline all impacting the player/coach relationship.
3. Introduce 'weighted' training camps, where you may look to work specifically on an area for improvement eg pass accuracy but it may have a negative impact elsewhere eg arm strength.
Perhaps this could be an added extra for the Co-ordinators who could pick 2 or 3 areas for the whole Offense or Defense to work on eg Zone Coverage and Strip Ball. How effective it would be would be based on a Coaches rating in that specific area.
4. Have a wider variety in playbooks. A new coach age 30 for instance would start with 40 Offensive plays and 30 defensive plays and would pick up one to three play(s) from each co-ordinator and two to five plays (minimum. one offense/one defense) from his Head Coach each season.
This would allow a Coach to start his career with a basic philosophy but pick up plays from his mentors each year. As such his philosophy could change over time
5. The option to match or improve an offer from another team in 'Free Agency'