I wonder whether subtle is a positive, neutral or/and negative word? Looking up its definition, it seems that the word means things unclear for good reason.
For example, I wonder if subtle can be used to describe a class that is not easy to understand? If so, would that mean more of that the class is difficult to understand because of the complexity of its content, or due to the inability of the lecturer?
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.
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.
This disregards the use of the word subtle in terms of organoleptic quality - i.e. a subtle taste or aroma. Subtle would seem to be positive in such a context compared to faint, say, or weak.
My impression of the word subtle is the opposite of overt, and could be described as nearly hidden, obscure or understated, requiring a deeper understanding of the writer's intent. Foghorn Leghorn remarks:
That's about as subtle as a hand grenade in a barrel of oatmeal.
