There are many changes between the 2.3 and 3.x versions of the score function. We believe they are all improvements.
Some of the specific changes:
A) count-pair has been modified to be more internally consistent: 3-bond atoms have 0 interaction, 4 bond has .5, and 5+ has full.
some residue pairs used to be spuriously unscored; that’s fixed
C) the whole etable (fa_rep, fa_atr, solvation) has been smoothed and its “range” lengthened a bit.