What they did to Flanders really sucks. He was a wonderful character. The Leftorium episode is absolutely heartbreaking, but gives Homer such an opportunity to redeem himself.
Those fleeting moments of humanity and growth were my favourite part of Simpsons as a kid.
I'd argue the show has worked their way out of this trope in the recent 5 seasons or so. Ned Flanders in recent episodes has figuratively grown a backbone: he stands up to Homer, he remarries a woman with a colored past, etc. His character has certainly evolved (possibly with awareness from the writers of this specific trope).
Those fleeting moments of humanity and growth were my favourite part of Simpsons as a kid.