In the original comics, the Time Scepter is normally associated with and used by Lord Simultaneous and his timestress apprentice Renet. They often encounter Savanti Romero. None of these characters appear in this film.
The only live-action Teenage Mutant Ninja Turtles movie that doesn't have the Jim Henson's Creature Shop involved with the creature costumes. This explains why the Turtles' and Splinter's appearances in this film are different from the previous two movies.
"TMNT: The Next Mutation" was a concept for fourth live-action movie should this third movie prove a success. In this concept the Ooze that transformed the Turtles and Splinter was still in their bodies causing a much more drastic 2nd mutation. Michelangelo's mutation would have gave him a more human appearance allowing him to walk amongst the people of the City. Donatello's mutation would have gave him to have psychic abilities, but have him wear an optic device because his mutation would cause his vision to deteriorate. Raphael's rage would cause him to mutate into a fearsome creature with claws and spikes jutting from his body. Leonardo would have the ability to mutate his skin into different textures. And Splinter would transform into a creature twice his size that he would have limited control over. However, the third movie was not as successful as hoped and the fourth movie was nixed. Concept art for the never made 4th movie can be found as unlockable bonus content in Teenage Mutant Ninja Turtles: Smash-Up. The concept of having the Turtles mutate into creatures was later used in the 'New Mutation' saga of the Teenage Mutant Hero Turtles cartoon. Later the "Next Mutation" name was used in Saban's live-action series, Saban's Ninja Turtles: The Next Mutation. Matt Hill, who voices Raphael, is the only actor from the films to reprise his role in the "Next Mutation" series.
In the Teenage Mutant Ninja Turtles franchise, "turtles in time" is the theme for the 1st Super Nintendo game, the 2nd arcade game, the 3rd movie and the 4th game made for Nintendo (the previous three were for the original Nintendo Entertainment System).