By counterproductive, I mean "discourages answering difficult questions in difficult subjects"
After answering questions on Stackoverflow for a few days and learning how things work, my first impression is that the reputation system is profoundly broken. Initially I was excited to build a high reputation, but now I'm feeling like the SO rep score isn't that meaningful. A few reasons:
Reputation is more easily earned on "easy" questions rather than "hard" questions. Race to answer "what does this keyword mean???" and get 20 up votes. Answer a subtle and difficult template metaprogramming question and get 2.
Reputation favors speed over accuracy This is pretty well understood, I imagine.
Reputation is more easily earned on subjects with broad appeal, rather than on expert level subjects I'm starting to suspect that if I want 10k reputation as quickly as possible, I should brush up on my PHP and CSS.
I think the reputation reward for an answer needs to be a more complex measurement than it currently is, taking into account the difficulty of the question (answer harder question = more rep), the popularity of the topic (answer a less popular subject = higher rep) and make changes to discourge quick, short, and wrong answers (perhaps have the rep rewards scale with time; downvotes count more the first n minutes, upvotes count less, etc).