It's not that your teammates are feeding berries only to the weaker pokémon, as I initially wondered, myself. It's that the stronger pokémon are 10 times hungrier.
While at first this felt like nothing but a vile nerfing of our best defenders, I now see two ways it can be useful. First, in the new gym defender prize system, a trainer receives 1 coin for every 10 minutes defended, up to 50 pokécoins per day, received when the pokémon returns home. So if your goal is to maximize your pokécoins to spend (rather than your time-in-gym for your gym badge bonuses), you may want your pokémons' motivation to degrade faster, so that they will return to you promptly with those coins! Second, if your goal is precious, precious stardust, then a hungry 3K+ CP pokémon in a handy gym could give you more total opportunities to redeem berries at 20 stardust per berry.