Grading by assigning points to exercises
If good students who understand the topic well are getting bad grades because they don't do all the problems, you should think very carefully about whether you've made the exam too long.

If this is what is happening (and I suspect it is), there is a very easy way to fix it: 


  Assign fewer problems.


Then you don't have to worry about coming up with a new kind of grading scheme that looks at the test as a whole, and which the students who get low exam scores will undoubtedly complain about.

If you designed the exam by looking at exams that professors had set in previous years, they probably also made the mistake of putting too many problems on the exam. It's a very easy mistake to make. I've heard the guideline that professors should be able to solve the problems on the exam in one third of the time that you give students, and I'm not at all sure that it shouldn't be less.