The imputation theory was important because it adressed the question of economic value. Marginalist economists such as Carl Menger and the Austrian School maintained that value was not made up of the factors that made up a good, it was made up of the most valuable use that the last good could be put to - or the marginal utility of the finished good.
While it was easy to maintain that this was the value of goods consumed by the end user (higher order goods), it was harder to make this case for lower order goods which had no end user and merely went into the making of higher order goods. In effect lower order goods do have end users, the manufacturers of higher order goods. It was these people whose marginal utility decided the factor prices, and their products were valued on their marginal utility to the end users. Thus the factors of production were as sensitive to marginal utility as consumer goods themselves.