The original one just has some parts taken out compared to the long version.
I'm the kind of nerd who'll go through and see what's different, so I loaded them up, converted them to mono, panned one hard right and the other hard left, then did whatever edits I needed to make them match up.
The standard version has a little bit of a riser effect to transition into the cuts. The mixing seems a little different between both versions, too, with the drums being a little more prominent in the long version.
EDIT: Just did the same comparison with Airbuster and Jenova Quickening. They're completely identical as far as I can tell.