We just pulled our son from a small, small school. What we found was that while his educational needs were being met, they were only training him in the 3 R's. There were no extras. No music, no art (until a mother volunteered), no PE, no character education.
Then we started seeing warning signs in the employees. They were underpaid and overworked, his teacher didn't get regular breaks.
Then we started looking at the administration and noticing that the people who were unhappy with the school were being called "crazy" or "too picky." Families had been leaving the school the whole time our son went there and it took us a while to see what the issues were and how they were effecting our son on a day to day basis.
In short, our school turned into dysfunction junction. I think that this is a regular occurrence in small schools. Ask around about the emotional health of the organization. Do families stay with the school a long time? Is there a lot of turnover? It is easy to recognize when children are learning and learning well, it is not always easy to see when an organization isn't working well and won't be a good long-term fit for your family.