Okay, while it's hip to pick on Meagan Fox, I think she's not bad looking, and while not a great actress she's actually passable. Rather than knocking her, I tend to at worst classify her as beautiful but forgettable.
THAT said if Michael Bay has half a brain the first thing he's going to do is pretty much ignore the cartoon version of The Turtles, even if that's what people are most familiar with due to exposure it's really kind of the worst version of something like this to do in a big budget movie, especially seeing as a lot of it was designed to sell toys and such, much like The Transformers, so stylizing things differantly makes a large degree of sense.
Unlike Transformers, Teenage Mutant Ninja Turtles had an existance before relatively mainstream success which was popular enough to give them the chance to be rebooted into the comparitively mainstream version that was beloved by young children and probably wouldn't hold up.
While I'd wonder at Megan as a casting choice for the cartoon version of April O' Neil, I think she'd actually work pretty well for a verion more similar to the ORIGINAL April O' Neil who was an urban antique shop owner (if I remember correctly, it's been a while) as opposed to a TV News Anchor. In the original version The Turtles behaved substantially more low key as opposed to like overt super heroes riding around in a mini-buss with artillery cannons they seem to never use hanging off the sides, in bright yellow colors, with a turtle shell on the front, and their name on the side (if I remember the Cartoon depiction of "The Turtle Van" correctly).
As odd as this probably sounds given the premise, I think the degeneration of the original "Turtles" movie franchise in part occured because they rapidly started to get too kiddie, and too goofy, to appeal to the cartoon audience. With the cartoon a thing of the past, something closer to the original version would probably work, featuring somewhat grimmer, more secretive turtles that behave more like Ninjas (and news flash, they kill people).
On a surprising level, if done correctly Michael Bay might be right for this kind of material, he's big on the huge scale, flashy fight scenes. If he can hire a decent choreographer and reign in his love of fast cuts and lens flare so you can see what's going on better, it could just work since the original comics were a not terribly deep, but action packed romp into absurdity, that was never quite as campy seeming as you thought it was going to get as a sort of counterpoint since for a long time The Turtles actually exhibited very professional behavior despite their personality foibles, and were largely viewed as an urban legend if even that since being Ninjas part of the point was nobody even suspected they existed for the most part. Thrown in with old school kung-fu fights where they battle and routine kill like a dozen or more guys at a pop. The aliens were still very much "WTF" occurances but, also behaved a bit differantly than the cartoons, more like something out of a horror movie, making them surprising even for the already crazy turtles rather than a "oh gee, it's Kang again... robots with laser guns.. passe", indeed the whole thing Kang is based on in the originals is substantially differant to say the least.
Just my thoughts. When you get past the whole "I hate Michael Bay and Meagan Fox", largely because of "Transformers", I think it's important to realize that despite how wrong he is for some material, there is stuff a lot of those same "problems" can actually be a plus with. Think something closer to the original Turtles (which less people have probably read than claim to have) and you can see where the director, and April casting choice kind of work.