These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
There's a very Les Yay scene between Asuka (playing the Virgin Mary) and Rei (playing Gabriel) during the Nativity Play. Quite frankly, it's impossible to miss. Either that or Asuka and Rei were sneakily insinuating that Jesus is Mary and Gabriel's lovechild.