Just watched the film tonight, and am pretty convinced this is a sequel. I've read the entire thread so far and there are flaws I'd like to point out in the nay-sayer's arguments (Not going to overanalyze or fanwank. This is based on logic):
Taken straight from the source (listening and typing): at the very end, Kaworu says, "また三番目とはね。変わらないな君は。会えるときは楽しみだよ、碇シンジ君。" Roughly translated into English: "The third [child] again. You never change. I look forward to the time I could meet you, Ikari Shinji."
For the record, I speak Japanese and have translated crap here a long time ago (evangelion chronicles, found here: [url]http://evageeks.org/forum/viewtopic.php?t=1390&postdays=0&postorder=asc&start=0[/url])
First, let’s examine the translation. If you only looked at "You [Shinji] never change. I look forward to the time I could meet you, Ikari Shinji", and only that part, it's understandable that you wouldn't put stock into the sequel theory-- after all none of it is indicative of a previous Shinji that the theory implies. Any explanation the sequel-theorists put forth could easily be dispelled by plausible alternative explanations (such as the "they met as kids explanation"). That all changes if you add in the first sentence, "The third [children] again/また三番目とはね".
The "[children]" I slipped into the translation is implied in the original Japanese, since the use 番目 following a number (e.g. 三) always refers to a pilot child in the world of Eva. It implies that Shinji had been the third child before this time, and that "before" is something that Kaworu has knowledge of.
The most plausible and probable explanation as to why Kaworu said something like that would be that Kaworu has seen Shinji as the third children sometime in the past.
As it is established that this is Shinji's first time in an Eva in this movie/universe, and that the pilot selecting agency (Marduk in the old series) selected Shinji as the third children recently relative to Kaworu's moon awakening, it is impossible that Kaworu is referring to the current Shinji when he says "again". Therefore he must be referring to a past Shinji-- a past Shinji who also was a third children.
The rest is obvious.
Another thing is the image put up by Otakucrave, shown at the start of the movie where they’re setting up the overall scene:
The size and posture of the outline is identical to that of the dead harpies at the end of EoE. Stuff like that just doesn’t happen coincidentally. If you see RoE as an alternate universe and not a sequel, there just isn’t any plausible explanation. The only things that could make that kind of outline are the Angels and Evas. Adam (presumed) is on the moon and Lilith is underground, and it doesn’t seem that either could make that outline/posture. Neither Eva 00 or Eva 01 should have been on the surface before the first encounter in the movie, and even if they were how likely is it that they fell down in that pose, and couldn’t get up, warranting an outline?
The outline could only be explained by the harpy theory, and thus the sequel theory.
Other evidence, though not as conclusive as the above two, include:
The red sea/red water (2I explanation very plausible, but notice the lack of mention of 2I in the movie. None at all. Doesn’t that strike you as odd?)
Streak of blood on the moon
What I’m really curious about is the series of coffins on the moon base next to Adam. Kaworu gets out of one of them. Who’s not to say that there’s a whole bunch of empty Kaworu shells in each of those?