When using a mehudar esrog is hiddur only determined by Halacha? Is personal preference also be taken into account?
Personal preference is certainly taken into account.
An esrog should be beautiful, and beauty, though it might possess some objective features, is in the eye of the beholder.
It is important for a person to be subjectively pleased with his esrog, and this is definitely part of the hiddur of an esrog.
Best wishes for Yom Tov.