Performance Appraisal is an overall assessment of performance of an employee and does not cover only the subject knowledge. Even if your employees skill level and knowledge of subject is good the he/she achieves higher score in those areas but remember they are always meant to be assessed on other parameters as well. There should be some general parameters like planning and organising, communication skills etc. and then there should also be some project or task specific parameters which can be measured by implementing a KRA (Key Result Areas) model. In a KRA model some task specific goals are decided on SMART principal i.e. Specific Measurable Achievable Realistic Timely, and these goals are mutually agreed my the employee and the manager with specific deadlines. Then at appraisal cycle these are assessed for completeness and scores are guaranted.
See atatched two images, this should give you a very good structure of 1) General Competencies 2) KRA stucture
Also, you can set parameters for performance measure under two broad categories Quantity and Quality