(Everything I'm about to write is speculation, but is based on my experience of working inside the Beltway for a bunch of years dealing with political appointees who manage bureaucracies.)

My somewhat educated guess is that all this happened in a series of TSA HQ meetings that got caught up in the old concept of "group think". I wonder what came first -- the 3-oz bottles or the clear baggie?

The motivations of the TSA leadership were --

1. Give the impression that you very carefully and scientifically "backed off" the liquids ban to be a "good guy" to the public and the airline industry;
2. Save face by accomplishing #1 without having to admit that the ban was a knee-jerk reaction and that the TSA was wrong;
3. Make sure this "threat" stays in full view of the public by creating the baggie carnival. Just telling people they could carry liquids without rigid constraints and inspection would have been admitting failure. They just simply couldn't go back to the "good ol' days" of pre-8/10;
4. Give the American people a way to "participate" in security by forcing each flyer to spend an extraordinary amount of time finding 3-oz bottles, a quart-size baggie, and generally spending way too much time worrying about this;
5. To finally have a way to require 100% shoe removal
6. Make things easy for the screener workforce and to create the theater whereby the screeners look like CSI forensic investigators carefully examining each & every baggie and its contents in excruciating detail.

Hollywood itself couldn't have come up with a better script.