TMNT started out as a joke, I think. It was a big parody of other things that came out at the time. Its creators always took it lightheartedly.
The thing that they really get wrong with this script is that they take this subject matter about the turtles, krang, the techodrome, bebop and rocksteady (yes these things are all in the script) way too seriously . It got really boring to read after awhile, there's no sense of fun and adventure that made the cartoon and the first two movies enjoyable to watch as a kid.
You can't take TMNT and make a LOTR type story out of it. They even put some half-assed plot about them being trained and all to fulfill from prophecy, or some dumb shit like that. They had some good ideas in there though, like the turtles being brought in to this alternate dimension from their original world where things are the same but different (like how the Star Trek reboot did it). They just need to take it alot less seriously.