Maybe it's just me, but I hear a string piece in the 2007 mix that I don't believe accompanies the original. There's also a slightly different vocal track in terms of the arrangement of certain harmony parts. All very minor alterations...all in all, the song pretty much sounds like a repackaged version of the original.

Obviously, the main purpose of the 2007 mix was to be used as the theme for the Rebuild of Evangelion anime. I'm pretty sure they just tossed it into the most time relevant single package for the die-hard fans.