When first recorded (1674), the air of indecision expressed by the term shilly-shally was rendered in much more recognizable form.
The picture we have is of some Caspar Milquetoast of the day standing irresolutely and murmuring, “Shall I? Shall I?”
In the course of literary evolution, the question became reduced to shally-shally, but was accompanied by a parallel change of vowel, retaining the form of the question, to “Shill I? Shall I?”
Ultimately both paths of alteration converged, yielding the present shilly-shally.