Or maybe both father and son will wear super-skimpy Kamui and fight to the death with scissor-shaped swords!
Kill la Kill jokes aside, if Gendo has to die, he'll either die at the hands of Yui (again) or through having his grand plans finally get unstuck on him, and go out with another "I'm sorry, Shinji" or a variation on it appropriate to the new continuity. But getting Gendo killed is all too easy - after all, he and Fuyutsuki were practically the most "natural" characters to sacrifice in NGE. If Anno really wanted to go for something different this time around, Gendo would live but, to quote the end of Cowboy Bebop, "he's gonna carry that weight".