Basically a first criteria with a list of tie-breakers. I'm mostly basing the order on the "theme" of Lord of the Rings, so feedback on the game balance would be good.
1. # of Rounds X # of Players (ie solo taking 4 rounds = 4, two player taking 4 rounds is 8)
2. Threat Cost of Each Dead Heroes
3. # of Encounter Cards in play and in discard
4. Damage Tokens on Remaining Heroes
5. Final Threat Level
6. Victory Points
Number of rounds is first because stalling is boring and isn't in line with the theme.
Threat cost of dead heroes is important, because heroes aren't thrown away needlessly in the books. They only die when necessary. I think there is also nice juxtaposition between the first two criteria. You want to finish the quest as quickly as possible while also preserving your heroes. Is it worth it to commit that one extra character in questing and bank that no engaging enemies will be revealed?
# of Encounter cards is the only way I can think of to reward players for the potential swing of the encounter deck (besides victory points which are actually probably going to be bad for tournament play since they are too few and will wind up being random boosts for some and not others). Basically more cards seen increases probability of fighting harder monsters, getting worse Reveal effects and Shadow effects. Other ideas (other than assigning points value to every card) are welcome. (I also thought about suggesting that each encounter deck be set up identically so the scoring would sort of be like duplicate bridge, but I think that would be a nightmare if there was more than one round)
Damage tokens, basically same as above with dead heroes. Except that I think it makes more sense to reward players who potentially saw harder cards than to reward players who are too cautious to put their heroes in danger.
Final threat level is last because I think the game (and books) are exciting when there is a lot at stake. I think it's silly to penalize players for getting in just under the wire in terms of threat, it makes the experience better.
Victory points are last because they are pretty arbitrary (as above).
So you go down the list until there isn't a tie.
I think Encounter Deck variability is the biggest problem. Thoughts?