Top 3, IMO, that aren't user-related issues:

1.  Coach hiring.  Savvy owners don't spend 2m on a hitting/pitching/bench coach because they don't have to.  There are 50 of them at any given time of BL-quality.   This creates a disparity between experienced/inexperienced owners that needs to be addressed.   Keep the rehire process as it is but, once that's over, all unhired coaches go into a pool with no positional/level/salary demands.   Let the owners sort out the levels and positions.   Cap salaries at 4m per coach(players have a max so coaches can) and make FI the most sought after job.  That will prevent jerks like me from hiring all the decent FI as BC so no one else gets one. 

2.  Advance scouting.   Savvy owners don't really need it.    Again, this creates a disparity between those who know and those who don't.  Change ADV to show projections for players NOT on a BL roster.   This would include HS, college, IFA and free agents.    The higher the ADV, the more accurate the projection.    HS/College/IFA budgets will determine how many players you see but will not tell you the quality of them.    IFA demands will need to be standardized(100k is a good starting point) so owners with low ADV won't be tipped off as to their quality.   Players on rosters can have projections based on ADV as it stands now.

3.  Player development.  I'd say it's pretty standard for almost all players.   Owners can make a small difference in maximizing(or completely wreck them) development but a good owner develops players in a pretty standard manner.   Provide some diversity.   At least three different patterns.    Have some develop early and max out 2-3 seasons into their careers(18, 6, 1, 0, 0 OVR).  Have some develop slowly and be late bloomers(3, 2, 2, 10, 8).   And keep some the same(11, 7, 4, 2, 1).    The more patterns the better but we need more than one.   Savvy owners can look at a 2nd/3rd year player they're considering in trade and say "This is what he's going to be" with pretty high accuracy.