I've seen End of Eva too many times, so much that I needed to buy Slayers to get myself out of depression.

Yes, it is a lot like the end of RahXephon, but Eva is a much more depressing restart of the world.
Spoilers ahead for those who actually haven't seen Eva (not that I believe such people exist).

To understand it fully: Humanity committed a great sin when they tried to create God by experimenting on Adam, thus the Second Impact occured. Human souls were no longer in great supply after mankind sinned so greatly. So, in a way, humanity had to restart itself, which is the human instrumentality project. The goal is to combine all of humanity into one body, just like the Angels. This body is Rei for those who didn't figure her role out. Seele wishes to combine all of humanity for absolute happiness, and Shinji is the only one who actually seems to be able to do it, because only he can pilot Unit-01. All that fucked up shit with the Eva series happens, and Unit-01 is crucified and Shinji becomes a temporary God. Shinji decides, after finally gaining enough balls to make a decision by himself, that humanity should not be one. Thus, All humanity is liquified except him and Asuka, in essence becoming a new Adam and Eve.

It is interesting to note that Asuka now has brown eyes instead of her typical blue, I've heard theories that she is now Asuka, Rei, and Misato all in one, which is why she is so digusted in herself.

That's the whole explanation on my take of The End of Evangelion.

As for Deus Ex Machina, I may be taking it the wrong way, in the litteral sense, but there is no convenient wrap-up in Eva, excepting Eps 25-26, which I have always taken since the movies came out as a single instant in Shinji's god-like state.