Focusing on control:
* Independent
* Autonomous
* Self-directed
* Free-willed
* Spontaneous
Focusing on humanness:
* Human
* Real person
* Living being
* Organic
Focusing on movement:
* Natural
* Fluid
* Graceful
* Spontaneous
Focusing on the puppeteer:
* Master (when the puppeteer is in charge)
* Director (when the puppeteer is guiding)
The best antonym for "marionette" will depend on the specific context in which you're using the word.