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.
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.:
Opportunities for Improvement - OFIs (Assessment Feedback Comments) The term "opportunities for improvement (OFIs or OFI)" refers to written assessment statements (comments) included in Baldrige assessment reports (e.g., individual-, consensus-, and site visit-level reports and Applicant Feedback reports) that describe [Criteria] requirements that are not addressed (i.e., gaps) or that could be more effectively addressed through process or illustrated through results. [Baldrige Performance Excellence Program]
The term has much broader and less formal currency.
Perhaps perfection/imperfection is the wrong set of words here. Perfection is defined as (OED):
The condition, state, or quality of being free or as free as possible from all flaws or defects.
Arguably, the intelligent system which "allows room for flexibility and adaptation" would be more perfect than one that does not. In contrast, a word like rigid seems to better fit your intended meaning:
Unable to bend or be forced out of shape; not flexible.
Some antonyms might include: lenient, tolerant, bending, or pliable.
If you want to use it in a sentence for a person, the phrase "warts and all" can be used.
e.g. Although not perfect, but you are good enough to be accepted warts and all.
If you mention the context, it will be easier to suggest words.
