KERS takes time to recharge, right? So how about letting the driver choose when to use it? Just design it so that, practically, it only has enough energy to be used for passing attempts once or twice (at most) per lap.
As for points, take a cue from an old game show: allow each team a "Joker" that can be used once per season - declare before the race whether the joker will be used (e.g. after practice but before qualifying starts) and the team's drivers (both) get double points for that race.
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