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.
Crazy Awesome: In the first version, this showed up sporadically. The rewrite may have more as it progresses, since as a consequence of its now-established ties to Nobody Dies, the Rei clones have had T!Rei's personality downloaded into them. They've since escaped the Reiquarium and are spread throughout Tokyo-3 in disguise. One of them is Gendo's secretary. At least one of them has kids per Word Of God.
Epileptic Trees: The rewrite has spawned its fair share of these, with many theories regarding things like Ari's real father and Rei's booty call buddy.
Slightly subverted, that. In the rewrite there are two sets of Shinji and Asuka (one of them being rescued from End of Evangelion). Gregg has stated at the end of fic the older set will get married, but the younger set will settle on being Just Friends. Of course, he has also published a snippet where several characters bet how long it will take before they become a couple, and Gendo gives himself three weeks to get them together...