I have mostly been playing historical leagues in the 60s and early 70s.
I haven't disabled any of the features and have to agree that it starts to get rather overwhelming when arbitration and free agency kicks in. I have realized that if I let the game manage resigning players from season-to-season that my team's salaries grow exorbitantly.
So I don't really have an answer for you as I haven't turned anything off - in fact I've turned features on: trading draft picks, trading drafted players in the first year which add to the complexity - and take away from realism.
What I have done to limit the amount I need to do is to limit myself to GM-only, have my assistant GM set budgets, minor league promotions/demotions and allow the minor league mangers to manage the other minor league options. I haven't noticed how much that affects the growth of my team, however.
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