There most fitting opposite (IMO) for perfection is imperfection. This however does carry some negative connotation. What I would like to express is that imperfection is actually a good thing.
What word exists that means "not perfect" and at the same time conveys encouragement and acceptance?
UPDATE:
An example sentence would be:
"Imperfection allows room for flexibility and adaptation." The context here is intelligent systems.
Best Answer
Many people describe imperfections, deficiencies, weaknesses, etc. as opportunities for improvement. The term is especially prevalent in quality management.
They do this "to express that imperfection is actually a good thing," looked at the right way.
Also as per your question, opportunities for improvement "means 'not perfect' and at the same time conveys encouragement and acceptance."
If you google opportunity(ies) for improvement, you'll get many hits, e.g.:
The term has much broader and less formal currency.