Funny thing about TMNT is that Shredder dies in the first "arc" of the comic and only comes back in sci-fi ways.
It was the cartoon (and subsequent cartoons) that (imo correctly) brought back the Shredder time and time again. I agree that the Shredder transcends the other TMNT villains and should be the focus.
As a kid I always wondered why Bebop, Rocksteady, Baxter etc were not used in the second movie. As I got older I assumed there was an issue with copyright or licensing but they still used April, Shredder, Splinter the Turtles and Casey in the last two films, so that does not make much sense.
Third movie was fun, but massively flawed, should have been material for the 8th or so movie!
I think the 2002 Turtles series got the ideas right for how to make the franchise move onto enemies other than Shredder, and the most recent series is doing a bang up job with the Utrom and Karai being big players on the villain front.
