1. Make the damn battery user replaceable! If you know it is depleting resource and you designed the phone to last longer, this should be the case.
2. Be transparent to the user. Show in Battery Settings how the battery is doing and whether or not the OS is throttling itself.
There is a third one, put in a bigger battery. I think Tesla does this with Model S. Be nice to customers.
/rant
- pissed off customer with a slow iPhone 6 that is probably affected by this.