I hate Michael Bay but I'm not convinced that this will be all that bad for the movie ...
Michael Bay movies tend to "work" when they're not much more than juvenile humour and action sequences. The more these movies try to develop characters, have a realistic plot, or explain (just about) anything the more they fall apart.
To get the Teenage Mutant Ninja Turtles "right" you really only have to get the sense of humour correct and mix it up with some decent ninja action. There will (obviously) be some things that will be brought into the movie because of Bay's involvement, like April will most likely look more like a prostitute after a hard night of work than a Television reporter