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It's probably the same reason the writers didn't have Baxter Stockman stay in the Technodrome and work for Shredder/Krang after he became a fly, it was easier just to use two mutants.
With Krang also usually staying behind in the Technodrome in most eps, it was usually just Shredder/Bebop/Rocksteady sent to Earth for schemes. Having a trio of bumbling villains is a lot easier than an army especially if they were to be defeated in every single episode, it's the same thing the pokemon anime does with Jessie/James/Meowth. Just have a trio of incompetent villains and save the "big" villains for select arcs.
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