The way the scores are displayed can have a big effect on how intuitive the program becomes. Any ideas that make the scoring more transparent will help people get higher scores.

Give notice when you marginally improve on your best score. There is currently nothing but rankings to delineate between similar scores, I've also seen decimals suggested to address this.

A score window showing relative progress in the different scored attributes; hydrophobics, packing. hydrogen bonding, etc. This would offer a great deal more insight into how your changes were affecting your model. Also, it would let people know which aspect they needed to work on most.

The ability to change the gradient for scoring resulting from tension. At high scores, the entire molecule is essentially green, making it hard to see where a few more points might be wrought from small twists. Being able to set the red and green thresholds would offer a better idea of where the molecule needed relaxing.