A thought on how the ending is:

Shinji has just allowed the world to reform the boundaries between human
souls thus recreating the world of pain and love that he so desperately
wanted to run away from in the beginning.  He turns and see Rei as a
'spirit' (for lack of a better word) and then disappear.  He then sees his
not-so-beloved Asuka laying next to him.

(following is the conjecture - don't flame me)
Shinji thought that the other people would reform around him as their wills
would do (just rise out of the ocean like Venus).  Nope, their bodies can
only reform the "old-fashioned" way.  Shinji now realizes that he is the
biblical Adam to Asuka's Eve (or Lilith?).  To him that's too much so he
decides to take all this out on Asuka (not actually wanting to kill her -
it's the only way he can react in a violent fashion).  Asuka, in a rare show
of clarity tries to comfort Shinji by placing her hand on his cheek.  This
does the trick.

With his hands now off her and she too realizing the situation states the
last line (which really could be seen as either "I feel sick" or "I feel
disgusted").

Anyway that's my story and I'm sticking to it.