Unfortunately, I haven't played Invisible War, but I've been told it's just as excellent as the original overall, but it lacks the depth that the original had in terms of storyline. But yeah, Deus Ex kicks ass.

And yeah, I was mainly considering the party's story. The way Jenova and Shinra intertwine do add something to the story that's not character-driven, although technically their roles in the stories are driven by their associated agents (i.e. Shinra - Rufus, Scarlet, Heidegger, Reeve, Turks | Jenova - Sephiroth).