I have to say that the ending was overwhelming and sad but satisfying in a
way..  I nearly cried when Asuka met her end (near death) in the final
battle (I thought she was gone for good the first time watching it,
considering Shinji's anticipation and hope for her in the beginning of End
of Eva.)

I understand that very end has been analyzed to death and most
interpretations are either a repeat or too far fetched.  However, I believe
in a more simplistic explaination for the scene of Shinji choking Asuka, who
is bandaged and badly beaten.  Through the series, the subtle romance
between those two is often suppressed by their immaturity and unwillingness
to compromise when conflict arises.  Shinji didn't realize how much he loved
Asuka until she was comatose as the final battle was approaching; Asuka
didn't realize how much Shinji loved her until the ending where they are
reunited, though Shinji's feeling's were so strong causing him to want to
choke her (but if you look closely, his hands aren't applying any pressure.)
Asuka says "I feel sick" as an honest message to Shinji of how she feels
(who wouldn't feel sick after nearly dying and almost the rest of humanity
around you perishing.)  What follows the ending is purely the audience's
imagination but I firmly believe 1) Shinji and Asuka are the "Adam" and
"Eve" and they've finally accepted each other.  2)  A very difficult road
lies ahead for both of them.  3) Humanity descended from Shinji and Asuka
will continue to be blanketed by darkness and despair, just like before.

On an unrelated side note, when watching the TV series, I was a little
disappointed after Kaji was shot b/c I kept anticipating Asuka's reaction to
it, considering he was her closest friend but it never showed Asuka's grief
and mourning.  In episode 22 or 23, Misato almost gave it away when she said
"Never Again" to Asuka questioning if Kaji was calling her and Asuka seemed
puzzled.