Is "subtle" a positive, neutral or/and negative word?

Solution 1:

The word subtle is usually construed to mean "hard to understand due to intrinsic difficulty". It would be inappropriate to use that word to refer to a course or a subject which is hard to understand due to the incompetence of the teacher.

Subtle is sometimes used to describe something which is overly clever, and therefore wrong or misleading. But this semi-ironic usage of the word is itself pretty subtle (heh), and depends heavily on context. In any case, this doesn't sound like the word you want for your context.

Solution 2:

Subtle is neutral. You might describe an argument or a solution to be subtle - meaning it's not obvious - but I wouldn't say the word put a particular bias on it.