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Lots of changes to the human characters as well as the Turtles.
Sounds like the eponymous heroes aren't the only characters who've been radically altered from their well-known counterparts in producer Michael Bay's planned Ninja Turtles movie. (Be advised that some SPOILERS follow.)
Latino-Review has a rundown of their problems with the script by by Andre Nemec & Josh Applebaum. Bear in mind, this is just that site's opinion on an unproduced draft, but the changes they cite are fairly substantial ones.
For example, in this version Casey Jones and April O'Neil are 18-year-olds and exes. The villain is one Colonel Schrader. The Foot isn't a ninja clan in this, but rather a black-clad special forces unit led by Schrader (caught on to the similar-sounding name yet?).
The Turtles, who are introduced in a Jurassic Park-style scene, use their shells a lot more when fighting. They're also the subjects of the covert government op Project Ares, which involves mutagens and altered species. There's a whole other sci-fi element to this story, including revelations about the villains and what's at stake for New York City.
