I can't recall if Gendo is killed in the TV series, but I don't believe it's ever shown.
And I don't necessarily mean "fuck you" to the fans in a negative way. I guess it would be more of a "fuck you" to the genre, essentially taking the fans along for the ride (I was not referring to the movie alone, but the series as a whole). And based on how many people seem to be upset with how the series plays out (subverting general expectations for such a premise), I'd say it's not the most absurd conclusion.
But yeah, I can also see some animosity coming through the movie as well.
As I said before, I agree that certain elements could be cut from the TV series. But establishing it as a "giant robot fights monster of the week" cut and paste premise (which you had mentioned in a previous post), and then slowly twisting and distorting it as the episodes progress is integral to understanding and appreciating the conclusion. And yeah, the Angels are basically just Anno beating his characters with a stick, but dammit it gets results!
And hey, I know it's not the most amazing thing ever put to film (although I would say that it is a visual and auditory splendor!), but I feel that it perfectly accomplishes what it intended to do, and it just so happens to tickle me in all the right places! 0_o