A few ideas for consideration
PLAYER TRAINING
The training algorithm should be reverted back to how it was before the last update as this current situation is untenable and makes little sense although the motives may have been good. The purpose of the update should not be lost however the method was ill conceived , lazy and really a band aid solution. There is a simpler and better way to achieve this aim.
Quite simply create a cap on the differential between white skills and grey skills , I would suggest maybe 150 as the mark arbitrarily. As an example , if a manager wants a particular white skill to be say 200 then every grey skill must be a minimum of 50. The system would automatically service any shortfall in grey skills per training once that situation is reached or the manager may choose to elevate the grey skills himself. There is a point where the training of white skills would not be bound to the grey skills so if a manager wants his players first white skill to be 340 then he must train all grey skill to 190 and after that other white skills are not dependent upon the grey skill improvement. This will not stop the creation of "mutant" players however they do become very expensive to create and maintain. I would suggest that unless a manager is willing to pay a lot of money to the game he wont be able to produce/maintain more that 2 or 3 such players and even that will have a severe impact upon the rest of his squad. It will become a balancing act for managers who want to create such players.
PRIZEMONEY
This is a situation that creates a lot of the problems in the game now. Reduce the prize money in tokens for Associations by 50% , the reds , greens and blues can stay the same , and redistribute these tokens as prizes for League competition. I would only reward the top 8 sides in each division with a token reward.
LEAGUE COMPETITION
If the rewards for finishing top 8 in a League competition are implemented then there is more reason to compete hard till the end of a season. I would also implement a slight change to the % reduction at seasons end. Top 4 lose 20% , 5 to 8 lose 15% and all are promoted. Bottom 6 lose 10% but remain at same level.
ASSOCIATIONS
I believe some of the measures already outlines may seriously curtail some of the problems Associations in its current form have created. I would also re instate that short lived idea of teams being evaluated on their top 14 players as this measure stops draw manipulation almost completely if not completely. I would only institute this for Associations and not for any other competitions.
I would also consider creating 3 tiers of competition in all levels of Association play and not stop at the Gold level.
PLAYER TRANSFERS
Upselling between managers directly is too easily corrupted and needs to be stopped immediately as it is not in the best interests of the game as a whole. Player transfer directly should only be allowed between teams of the same level so upselling / downselling cannot occur. This is nothing to do with the Negotiation feature in the game.
ACADEMY PLAYERS
It would be a good feature for managers to have some input into what type of player their Academies produce for them. I would make a payment schedule that was dependent upon how much input from a manager. For eg - player between 76-80% - no input 10 tokens , primary position - 15 tokens , 3 white skills enhanced by 20% -15 tokens , 1 SA 50% trained 20 tokens , 1 extra position 50% trained 20 tokens.
TACTICS AND FORMATIONS
This is an area of the game that has been forgotten and needs to be revived. Tactics and formations are a large part of managerial duties and should be again in this game , maybe a value of an extra 5% for each which may help diminish the roulette type of results that are becoming more common. Some matches you do everything you can to ensure a victory while the other manager does nothing and yet you dont get the result you deserve. Upsets happen for sure but not with the current regularity in this game. Maybe more emphasis on tactics and formation will help to redress the balance and besides will make the game more fun.
Just some discussion starting points.