I do find it ironic that in retrospect since 1991 there have been a lot more violent films for teens and kids. TMNT II is today seen as pretty much harmless a movie. It is possible that at the time due to the nature of the TMNT property Henson's family were embarrassed to have the TMNT name associated with his last project. Kind of like how critics or viewers don't want a respected actor's last film to be a Michael Bay Transformers movie or something like that.
Dammit I'm sure Farscape is the key to all of this:
