Even when I was little I wondered why Bebop and Rocksteady weren't in the TMNT movies, and i didn't get an answer until after i finished college and began working on the TMNT cartoon (2003 series).
Tokka and Rahzar were created by Kevin Eastman and Peter Laird to get around rights issues with Bebop and Rocksteady.
The reason Bebop and Rocksteady (along with Krang etc) were not in the movies is because the movie studio and even the creators of TMNT didn't have the rights to those characters and didn't want to pay to use them.
Bebop and Rocksteady were not in the original comics and were created specifically for the 87 cartoon, and were owned by the show's production company. (Krang was inspired by an alien race in the comics called the Utrom, but was still considered off limits in this case).
It wasn't until recently (after a long legal battle) that the rights for these characters were won by Mirage/Peter Laird. Shortly after the win a direct to DVD animated movie "Turtles Forever" was created which featured Bebop, Rocksteady and Krang - and even had cameos by Tokka and Rahzar.
Shortly after the movie aired on TV Nickelodeon bought the Ninja Turtles from Mirage.
The shows original theme song is still owned by the 87 cartoon production company (which is why it wasn't in any of the movies despite being super popular) and they won't part with it without a ton of money - so while you may hear some sound alike stuff in the current Nick show you'll probably won't hear the original song used for a long time in any new media.
It always seemed strange to me that they made Tokka a turtle because A) The heroes are turtles and Slash the evil ninja turtle already existed at that point. You literally have every animal in the world to choose from or existing characters from the comics (like the alligator Leatherhead).