I can't help but wonder what the thought process behind Chess Mentor is. You learn something new, but are punished in the process and lose points, because you didn't know how to do it yet. It's like telling someone not knowing something is a bad thing.

Even if you have a good idea and it works out, you get punished because you didn't follow the exact plan mister author had set out for you. The only way to gain points is to either get lucky or to do a lesson you already know the answer to- but then, what is the point of having these points awarded to you anyway? 

Wouldn't it be better to leave the entire point system out of the Chess Mentor, and instead leave the big red "INCORRECT" sign to discipline the user? That way one would be free to read the explanations and actually increase their knowledge and understanding without feeling like they suck because their score keeps dropping.

The points are designed to measure your chess skill. It's called ELO. Chess Mentor adapts to your skill level and provides you with lessons that match your rating level so that you can get the most effective lessons possible.