The pilots' flaws are that they are not fucking Jesus incarnated at age 14 to deal with the fact that they have family issues in steroids and have to fight weird monsters who do weird shit.
The people who really should have been shot are Yui, Gendo and the rest of the science niggers who made the world shit because they couldn't control their curiosity boner wirh Adam.
I understand that the main point of the series is forgiveness and empathy but everyone in Nerv should have come out of the LCL with a bitch face towards Gendo and other top dogs after realizing they're entirely the ones to blame