Someone asked if Rei picked up Shinji's SDAT music player at the end of the movie. In the last shot of the SDAT, Rei is shown next to it, but it's never shown that she picks it up.
Up until that moment in the movie Rei is only following orders, literally, if there is no command she wouldn't do anything. So, taking into account that nobody orders her to pick the SDAT, that would be her first freewill act –if she is showed later to have done so, so far there is no evidence.
As for WILLE. They are not so heavily merchandised as NERV, so I could only saw in detail their logo once, and it's written like that, with no hyphen – which I assume was a pun started because of Wall-E.
The last impact at the end, ignited by Evangelion 13, is very confusing, but the key point seems to be that there are not spears, Longinus and Casious, but two copies of Longinus. I'm not sure about the chronology and details involved, but I understand that the mechanism is indeed the kind of impact SEELE wanted to do in Neon Genesis Evangelion with Kaworu: the Lilims will become one and revert to nothing, and Earth would be left to Adam's descendants. The result is the same as in Neon Genesis Evangelions, Kaworu declines to do so, so Shinji can as a lilim can continue to live.
For the most adept to details, there is a flashback –the shogi scene of Fuyutsuki and Shinji– about Yui's fusion to Evangelion 01 core. You may recall that in Neon Genesis Evangelion,
Lilith was jointed to Evangelion 01 in that experiment – I assume that Evangelion 01 was created through mitosis, but I'm not sure if is canon –. However, in Evangelion Q flashback it's shown the Evangelion 01 in a very similar structure, but you can tell is not jointed to Lilith. However, the fundamental logic behind Lilith's resemblance to Rei, and thus Yui, seems to be the same as in Neon Genesis Evangelion.
All crazy spoilers in this thread are true: the time lapse, Touji's sister, the curse of Eva (why Asuka seems young), the flying ships, etc. Except for that fake spoiler of Asuka being the last angel, it's never said during the movie.