At Your Own Pace
Have a practice mode where the notes do not scroll unless the note/chord is played, and when the selected region of the song is completed, grade how well the player kept on tempo. This way the player can practice playing the song without needing the game keeping rhythm for them.

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Unanonymous commented
I get where you're coming from. This is however against everything I've ever learned about practicing an instrument. Keeping steady rhythm is what you always do, even when practicing scales or other things that have no musical meaning by their own. Break it down to phrases and practice those slowly, then connect them and speed up. If you're practicing with jerky rhythm, you will learn jerky rhythm, not a steady and flowing one.