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Kevin Munroe (the director) and Tom Gray (the producer) explain (in the Super Hero Hype interview) that the reason was because no studio wanted to do another live-action TMNT movie, feeling that the (live-action) franchise was dead or had been done, also noting that the movie would've been insanely expensive done live action (another reason the studios passed) but when they pitched it as a 3D-modeling animated picture, it was easier to shop around as they would be able to accomplish everything they could in a big budget live-action film but at a fraction of the cost thanks to CGI.

Final Fantasy: The Spirits Within cost a phenomenal amount of money to make, and was considered a colossal failure that resulted in the director being fired and the company being bought out. Conversely, Final Fantasy VII: Advent Children was aimed at a very focused audience, where resources could be dedicated and still have the film be successful. This is not the approach the directors of TMNT wanted to take. They wanted to stay true to the original story, while still appealing to a wide enough audience in order to make money. In doing so, they felt that a more stylized rendering (rather than a more anthropomorphic and more photorealistic such) would help the film's success.

It is a loose sequel to the original films, much like Superman Returns is to the first two Superman movies. It takes place after the first movie. Parts of the second and third movie are acknowledged (such as the appearance of the ooze canister from the second movie and the Time Sceptre from the third) on Splinter's trophy wall, but it is unclear how much of those two movies is considered canon at this point. In the same image, it is unclear whether the canister that contained the "ooze" that mutated the Turtles and Splinter is marked "TCRI", as in the comics and the 2003 cartoon, or "TGRI" as in the second film.

Kevin Munroe has stated that they are in the age range of 18 to 19 years old: we never specifically set an age. I like that 18-19 range of just becoming a real adult on your own, etc. It's the kick you out of your nest point in your life. Good character drama age. [written here]

The Shredder is pictured very briefly in a recap at the beginning of the movie, but does not appear in the story itself. Director Kevin Munroe says:

As for Shredder in TMNT, yeah, I saw a lot of people saying he'll be making a cameo. We have nods to him in the film, but there isn't a scene with him or anything. But again, I wouldn't say he's gone from the franchise...

Producer Tom Gray (in the IGN interview) stated they had felt they had done Shredder to death by this point with comics, TV shows, and first two movies, so they wanted to take a break from him so they could use and introduce some other villains. There is a hint that the Shredder may appear in a sequel, and Munroe has more to say on that point in an interview (reported here):

Because we now have these sort of better Shredder stories of how to bring Shredder back. But now if it works out well, and Karai coming to New York, that's a setup for a really good volume in The Turtles in the comics as well, it could work out to a really cool sequel.

He is referring to the City at War arc from the Mirage comics, in which Karai temporarily takes on the mantle of the Shredder. So it is possible that if we see the Shredder in a sequel, it will be Karai and not Oroku Saki wearing the armor. This is supported by past statements by Peter Laird that he does not want Saki to return.

No. While Mirage does own the rights to those characters, Peter Laird wants to keep this movie true to the mood of the comics, the first movie, and the 2003 animated series, and as far away from the original, campy animated series as possible. While a number of people have claimed that Mirage doesn't own the rights to the cast from the cartoon, Laird had this to say when the issue came up in the 2003 animated series:

It has been stated a number of times in various places that the reason the new animated show does not feature Krang, Bebop, Rocksteady and the Technodrome is that Mirage does not have the rights to those characters. This is not true. We have the rights to those characters and most of the other characters from the old animated series. The reason they are not in the new show has NOTHING to do with rights issues, but rather the fact that I did not want to use them. [source archived here]

Yes, led by Karai (taking over from the defeated Shredder).

April, Casey, Splinter, and Karai.

Karai takes over leadership of the Foot after the Shredder's defeat. She first appeared in the original Mirage comic series and can also be seen in the 2003 animated series.

While it is unclear when April quit (or lost) her reporter job, the prequel comic establishes that she got the archaeology job as a result of her work at the Second Time Around antique store. Max Winters approached her and was impressed by her expert knowledge, so he employed her to seek out the artifacts he was looking for. It is also worth noting that April was never a reporter in the original comic series or the 2003 cartoon series.

As stated before, the turtles are now 18 and 19 years old. In the original films, they were 15 and 16 years old. So, in those three years, April has been training under Master Splinter.

Not exactly, but the movie isn't very clear either. The following scenes are presented in the order that they appear:

(1) We see Winters overlooking the captured monsters. There are three empty spaces. (10 out of 13 captured)

(2) Raphael and Casey witness the Generals capture the flying monster. (11 out of 13 captured)

(3) General Aguila told Winters that there are two more monsters left, which is correct by our count.

(4) General Aguila then tells the other three generals that they shouldn't find the 13th monster if they want to live forever. In this scene we briefly see the generals forcing some sort of monster with tentacles into a cage. Now, here is where it gets confusing. We could assume that this is the flying monster that they just captured, however the flying monster did not have any apparent tentacles on it. If this was a different monster, then that would bring the count to 12. However, we could also rationalize that either (a) the flying monster did in fact have hidden tentacles or (b) this was one of the previous 10 monsters that was trying to break out.

(5) Raphael battles with the Jersey Devil in the diner.

(6) Leo is then captured by the stone generals and is used as the 13th monster.

(7) Later we see that the Jersey Devil has since been captured off screen along with Leo. (12 out of 13 captured, Leo not counting)

(8) At the end of the movie, the 13th monster is delivered via the Cowabunga Carl van to the swirling vortex. (13 out of 13 captured)

So, while there was no blatant plot hole, the fourth of the aforementioned scenes makes this questionable.

Munroe stated they tried it, but it looked too weird:

I knew I'd get this question sooner or later. We actually tried a version of it. It looked okay if you knew the origin of the story. Otherwise, it looked a little strange at first glance. It was a conscious decision to go full-eared. We just added a line about his otoplasty procedure and how it improved his self-esteem, finally enabling him to love again. Aww. [written here]

Peter Laird was closely involved with the project. Kevin Eastman was not involved in any official capacity, as he sold his creative stake in the TMNT property to Laird several years back, but claims in a Newsarama interview that he helped with the initial deal and had regular contact with Kevin Munroe during the process. (Source archived here)

There's a brief but very thorough rundown of all the TMNT comics on Newsarama (archived here). The official TMNT website was ninjaturtles.com. It contained the most comprehensive information likely to be found on all things TMNT, and in addition to summaries of all the comic series (Mirage, Archie, Image, Dreamwave), it had the first ten issues of the original series, as well as Fugitoid #1, available in their entirety for online viewing. The Internet Archive has snapshots for #1, #2, #3, "Raphael", #4, "Fugitoid", #5, "Michaelangelo", #6, sans "Donatello", and #7. A new issue was posted roughly every two months. The ninjaturtles.com site also had a catalog section (like so)—low-tech and required that an order form be printed out and mailed in, but there were some great deals there. Back issues are also available at comic sites such as nostalgiazone.com. For current issues of the TMNT comic, including the miniseries that leads up to the new movie, support your local comic shop.

There is Shredder's mask, the Time Sceptre from the third Teenage Mutant Ninja Turtles film, the Honor Guard helmet from the third film, Walker's hat from the third film, A Mini-Mouser from the animated series, The Honor Guard suit, one of the Honor Guard swords, and Winter's helmet.

Imagi used Maya, with Pixar's RenderMan for the production pipelines back-end.