GHOST IN THE HUMAN REVOLUTION:
Instead of embarking on a psuedo-academic rant, I've decided to go for something much more subdued. I have chosen five categories, and compared the two franchises on them. For the sake of brevity, I have
ignored the original Deus Ex. Also, I have chosen to focus on the more recent Ghost in the Shell: Stand Alone Complex, rather that the 1995 original.
Ghost in the Shell and Human Revolution both explore the concept of human augmentation. Theseus' paradox is more notably explored in Ghost in the Shell, because in GITS, human existence can be transferred from one vessel to another. In Human Revolution, even the most heavily augmented characters still have at least their human brains.
Adam Jensen is a security agent who becomes mortally injured. This bears some similiarity to the Six Million Dollar Man\Inspector Gadget archetype.
Motoko Kusanagi has been a cyborg since early childhood. This sets her apart somewhat from Jensen. He is post-human, she has arguably never had a chance to be human.
Michael McCann's throbbing, synthesizer driven soundtrack is similiar to Yoko Kanno's soundtrack for Ghost in the Shell: Stand Alone Complex. But it also bears similiarity to Daft Punk's Tron: Legacy soundtrack. Of note is the theme song, which plays during the credits. The rising and falling vocal harmonies are akin to those of Inner Universe, the theme song from Stand Alone Complex.
Where the two significantly differ is the incidental tracks. Where Ghost in the Shell shifts from electronica to heavy rock for action scenes, Human Revolution never loses consistency.
Human Revolution is heavily influenced by Renaissance art. Ghost in the Shell is somewhat different. Its art style is more gritty, washed out, compared to the specular and bloom heavy Human Revolution.
The art style of Human Revolution gives the world a dreamlike appearance.
One thematic element which links the two together strongly is the combat scenarios. Just like Kusanagi, Jensen often finds himself trapped in buildings being stormed by cloaked forces, supported by mechs.
The idea of viruses, hackers, or bugs affecting augmented humans and driving them crazy has parallels in GITS, both franchises tapping into the primal fear that technology might be capable of stripping away free will.
I wish I could have written something better than this somewhat thin article. Perhaps I will at some point. I've just been so busy and distracted recently. I hope this article is helpful to someone.