There’s a lot of subtleties in 3.0, one of them being Anno’s use of spacials and dialogue to ‘shift’ the main cast across one generation. Misato takes on a role that was originally Gendo’s (emphasized further with her visual upgrade, unfeeling shades and all), and Ritsuko takes on a role that was originally Fuyutsuki’s – others have already pointed out that this “evolution” was quietly alluded to during 2.0. (And by extension, Gendo and Fuyutsuki have adopted SEELE’s role upon SEELE’s demise, Asuka has adopted Misato’s role, Mari has adopted Kaji’s role, so on and so forth.)
It’s hard to say what this will mean for 3.0+1.0 – especially in reference to Misato and Shinji’s now-broken dynamic – but it’s definitely worth noting (and speculating) on anyway.