I think that Competencies in Moodle 3.1 is exactly what you need, because :
1) Grades are only in the course (not platform wide), and it would be difficult to agregate many grades from many courses in a synthesis way to say for example "This student gets 70% of the skills".
2) Outcomes are fine, you can associate a scale to each outcome, use Assignment for evaluation and see them in the gradebook, but like grades, outcomes are not platform wide.
Competencies in Moodle 3.1 are a very powerful tool and we need changing a bit our teaching habits but :
- Competency Frameword supports hierarchy between skills
- Different Scales may be associated to different Competencies
- Learning plans may be associated to individual users or to cohort
- Competencies are platform wide and, better, category wide
- Competencies may be evaluated through activities
By the way you may transform your Outcomes list and scales to a competency framework.
PS: Excuse my poor english...