I find the origin to be, for lack of a better term, too serious and too short. It took from RISE OF THE PLANET OF THE APES and THE AMAZING SPIDER-MAN in an effort to be clever, forgetting that the origin was fairly simple and cartoonish to start with, and ended up becoming a half-baked mess.

Beyond that, it deserved more than a flashback to explain it all. We already had a flashback in the 1990 film, we could have had an origin story and a cut to 15 years later.

Anyway, here's how I would have done the origin: Open at the TCRI Institute. Research is going on a new compound called mutagen; scientist Dr Kirby O'Neil (who brings his daughter April to work) theorizes that it has the power to splice DNA of different species together, creating a hybrid race of soldiers that possess superhuman abilities. The Institute is taken over by Eric Sacks, who runs the Foot (second to the TRUE Shredder), who has taken interest in the mutagen and its properties. He publicly executes Hamato Yoshi, a former samurai who defied the Foot and refused to pay them tribute, to use his warrior's blood and to make an example to the public. The blood is mixed with mutagen and tested on a lab rat, and it is proven to be a success: the rat's intelligence has improved and he can read and write. However, he has also inherited the genetic memories of Hamato Yoshi...

The Foot next brings a set of four turtles who are also injected with the mutagen. However, Dr O'Neil decides to destroy the mutagen so that no more biological weapons can be formed from it. Sacks kills him, but a young April manages to set Splinter and the Turtles free and is then put into a foster home. Eric Sacks decides to be her guardian, nothing she has no idea he killed her dad, and thinking she may know something about the mutagen...

... then cut to 15 years later and leave the rest of the film as it was.

That's how I would have done the origin. Nothing really too fancy, just an idea I had. I hope you guys will like it.