For whatever reason, the American bishops have tended to be a weak-kneed bunch, and their bureaucracies are full of liberal dissenters who undermine them whenever THEY try to clamp down. The Pope has replaced most of the worst bishops with better ones, but too many of them still lack the will to do what needs to be done. The Church in America was badly hit in the great countercultural revolution of the 1960s and thereafter, like all our other institutions. On the whole, it has done pretty well, considering the grave damage that liberals have done from within. Many of the Protestant denominations were similarly affected, and many of them have had more trouble recovering from the damage than the Catholic Church has shown. They also have homosexual problems, but the media ignores it, or applauds it, because they consider these churches to be too weak to be a threat to their desire for "sexual and reproductive freedom."
Of course, he could have excommunicated a bunch of people, but I'm not sure whether that would have been more productive than the course he has taken. You can't run a Church without the willing cooperation of the hierarchy, the priests, and the laity.
JPII has to walk a tightrope. How does he do his job of reprimanding needed individuals and not stir up events that might lead to an even deeper apostacy? And not scandalize the faithful in the process? I believe he is the very Pope who Bosco saw in his dream guiding the huge ship of state through the tremendous storm to a safe harbor.