I have a question for anyone who has dealt with consistent 2nd half collapses during a season. My team is routinely winning, and many times by double digits at halftime, but ends up winning nail biters against average teams or losing to good teams who have monstrous second halves. I've fiddled with game settings all season, but nothing seems to help. It seems like my team just starts the second half flat every game, but i've also had a few games where I was winning by double digits with less than 10 minutes in the game and my team choked down the stretch.

By all accounts I should be at least a top 50 team (as I have consistently been the last few seasons), but I'm scraping the 100s. I have my playing time set by minutes rather than fatigue, could that be an issue? Any advice on how to maximize second half play in general, not just the last few minutes, would be appreciated.

Teams that consistently fade down the stretch generally have stamina issues, leading to fatigue, fouling out key players (which is a result of fatigue) leading to more fatigue on the rest of the team. After looking at your team, this is exactly what has happened. 

using minutes instead of fatigue can definitely be the issue. Some folks use minutes successfully, but in general a rule of thumb is to NOT plan for the whole 200 minutes - leave everyone like 1 category short of where you'd put them for 200 that way the engine will be less likely to have to stretch a fatigued player to meet minute demands.