evangelion (and its manga series) were committed to realism to the extent that family members actually looked biologically related - in general, this is difficult to achieve in any animation medium, where stylistic convention can contribute to same face syndrome. 

shinji is a perfect composite of gendo and yui’s features, but in a natural, effortless way - he’s not a random synthesis of “gendo’s eyes” and “yui’s chin” or whatever. rei looks like a young yui, but again the facsimile isn’t forced - it’s just enough to color naoko immediately suspicious, but not enough to arose suspicion from everyone everywhere. ritsuko and naoko share the same power brow and pointed chin - the show even went out of its way to explain ritsuko’s blonde hair as a result of repeated hair coloring, a slight of authenticity not often broached in anime. in the manga, kaji and his younger brother look so alike yet apart, and you can easily pick them out from a crowd of other nameless kids - this is really impressive, considering the medium.

rebuild isn’t interested in having relatives’ looks cohere. sakura and toji don’t look related - which is especially heinous considering toji’s looks are so pronounced and iconíqq (flat chin, dark skin... compared to sakura’s boringly petite and pale features) anno is on record saying his only goal for sakura was for her to be “cute”, so maybe he thought he couldn’t succeed if she looked too much like toji. trash.