One somewhat strange feature of NeoLemmix is that completion of a level is awarded a score based on a complicated algorithm whose details are hidden from the player. In theory, this allows another dimension for competition / challenges. In practice it seems to be ignored; there was a topic in Challenges for best scores on the original levels, but it quickly died, and nothing similar even got started for custom levels.
One possible reason is that Lemmings just isn't the right kind of game for a numerical score -- it already has a natural metric for comparing solutions, namely number of lemmings saved. (Simon has claimed that no-one cares about scores in any game, but this is certainly false.)
So there's a question whether the scoring system should be kept into NeoLemmix 2 at all.
If it is kept, my first suggestion for improving it would be to allow pack designers to customize the algorithm -- i.e. they can decide what to take into account and how many points each factor is worth. For instance, if I were to do a pack I'd like to use a simpler system. Pack designers who don't want to have a scoring system at all could disable it. It wouldn't matter that the algorithm would vary from one pack to another, since comparison of scores across different levels is meaningless.
Also, I suggest that if it's kept, the scoring system should be made more significant. The game itself could keep track of your best score for each level, and display it under the score just achieved on the post-completion screen. Achieving above a score threshold could be one category for talismans.