I have just 2 seasons under my belt. I had the same problem in my first season. In the second season I made a plan for each individual player based on durability rating and experience with the player. I had no issues. Also 99% is an arbitrary number that you are using, however that absolutely is not tired. You want to avoid getting to point where you are forced to rest players. Some tactics that worked for me:
1. Limit exposure for Veterans during Spring Training
2. I had a 21 year old rookie player in just his 3rd pro season, I left in the minors for the first 20 games, only actually playing him in the last 5 games of that 20.
3. I bookend off days with rest days so lower durability guys get 3 days off instead of one.
4. I rest players for unfavorable match ups. ing . My catcher is my best hitter, he has low durability ratings, I held him out most of the spring, used the bookend tactic and rested him for the series before and after the AS game.
6. If the standings allow, I rest players against the lesser teams.
7. Have a good 4th outfielder and 5th infielder. my 4th of had over 300 ABs and 5th infielder had about 350 ABs