you would find a number of theoretical literature that would give you alternative approaches to evaluate innovation systems performance. search these articles for instance
- Systemic instruments for systemic innovation problems: A framework for policy makers and innovation scholars;
-Rapid Appraisal of Agricultural Innovation Systems. A diagnostic tool for integrated analysis of complex problems and innovation capacity
- Structural Conditions for Collaboration and Learning in Innovation Networks: Using an Innovation System Performance Lens to Analyse Agricultural Knowledge Systems