If I set my lineup to strictly follow depth chart then I do not understand why my team constantly ignores that fact in the 4th quarter when I am winning big. I think a change in the substitution algorithm would be beneficial in this circumstance.
Another option would be to add another pre-planning decision that lets you pick a point differential and time amount left in which to pull starters.
For example I could tell my coach to pull starters with a 30 point lead and 3 minutes left. This would not always be exact but it would help.
Having a higher PD can be very important and I grow tired of a game like today in which my 25 point lead to start the 4th drops to 12 by the end due to my starters playing 0 minutes in the 4th quarter. I would hate to lose an important spot in the standings at the end of the season due to something that I can have zero control over. This is my only real beef with this game at the moment.