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Prior to the scandal, the local bishop was in charge of all administrative issues and with dealing with the civil authorities. Moral theology was overseen by the CDF. For example, if someone in Boston were to teach that pederasty is a legitimate sexual behavior, CDF would point out that it is a false doctrine. If someone were quietly molesting altar boys, the local bishop was supposed to deal with it since no theological heresy had occurred.

This explanation seems to me to ignore the process by which a bishop becomes a bishop. While my reading indicated a somewhat complicated process, two key elements were that approval was required by the appropriate congregation of the Roman Curia (Vatican) and that the actual appointment was made directly by the Pope. The Vatican cannot simply install these people and then wash its hands of everything they do or don't do.

The attitude I seem to be getting from apologists is that the Vatican/Pope chooses the bishops (who then choose the priests) but after that all bets are off and the Vatican/Pope then bears no responsibility for what happens later. For example, you said:

That the Pope is ultimately in charge of this matters is half the truth. He mostly works through delegation to bishops who are sovereign in their dioceses. While he can in principle dismiss a bishop, it is a highly unusual thing to do, and we Catholics don’t like innovation.

It's not a half truth if the Pope CHOSE the bishop in the first place! :) Of course the Pope is ultimately in charge because he chose the bishop, has FULL authority over him, and the at-will right of removal. Given the scope of the scandal I find the rarity of removal to be damning rather than exculpatory. It gives all the appearance of the Pope not wanting to admit a mistake and doubling-down on a wrong choice made.

Absolutely; this is why Pope John Paul II shares some of the blame. Our topic is the culpability of then Cardinal Ratzinger, and he wasn't pope then. With the few scandals on his watch he dealt resolutely.

I am simply pointing out that a bishop, once installed, receives a very wide lattitude in how he administers his diocese. In the case of several latently homosexual bishops it proved unfortunate.

Note please, that the strict control from Rome that you correctly say was lacking during John Paul II pontificate is the exact opposite of Protestant ecclesiology, which produced the same rate of abuse but rarely faces the consequences of it.