I would argue that Kyle is more intelligent than Stan. While some say that Stan is "street smart" while Kyle is "book smart," I haven't really seen him do anything that struck me as more intelligent than Kyle, academically or otherwise. I'm not sure I would call Kyle the most intelligent (him and Wendy seem to be more or less tied,) but in my opinion he is smarter than Stan.
As for the most intelligent... maybe Garrison's dad, honestly. He was the only adult in South Park who though it was wrong to molest your child, after all.