[Boshusan]

In Dairanger, most of the important Gorma are just clay dolls and are not aware of their condition, there was someone or something else behind the curtain.

In Shinkenger, the head of the clan was not ShinkenRed but a girl, he was a decoy. Too bad she appeared too late from nowhere, but the idea of a female Red could be fresh and awesome for the super sentai formula.

In Liveman, Dr Bias intended to use the brains of his evil geniuses from the start, to be young again. There was an aborted plot with a timeloop/time travel that could have been about Bias indefinitely get old and get young again, this would have been awesome but the last episode discarded that part.

On a much more personnal level, in Bioman Prince was a replacement for Dr Man's real son. At the time I watched this I was 7~8 old, and it really freaked me out when it was revealed he was not his son but an android, and he didn't know himself; and later the real son appeared in the show.