Skill issue is a term used to denote a lack of skill and need for more practice. It's mostly used in the context of computer and video games when somebody asks how to accomplish something and the answer is best summarized as get better at the game. Obviously, this is not what people asking for help want to hear and it makes for a discouraging response. Being a discouraging response makes it an excellent go to for trolling. Thus was this top tier dismissal born.
As far as infuriating responses go one of the strengths of saying "sounds like a skill issue" is that it's often true even when there is useful advise to give. It's almost tautological in its applicability since any problem that a person asks for help with is going to be something that a more skillful person wouldn't ask about. There could be a very simple fix but if the petitioner doesn't understand their issue they won't ask the right questions. This is a fully general issue with asking or answering questions in the contextual vacuum that is online chat. The temptation to offer a probably correct, fully general, stock dismissal to a badly worded, overly vague, drunk post of a question is strong even in naturally helpful users.
The other major advantage of "skill issue" is that it's humorousness scales with its inappropriateness. Any complaint can be described as a skill issue and the less control a person has the funnier it is to claim that they just aren't trying hard enough. Car broke down. Skill issue. MacGyver would fix that in three minutes. Bad date. Skill issue. Learn to cold read people through their EHarmony profile. Dying of cancer. Skill issue. Use your chi to sooth the tumor. You can't parry an explosion. Skill issue. I don't even feel the need to explain this one.
This is where the real power of the phrase lay. It works for ever situation. Big or small, true or false, justified or wildly inappropriate it always works to answer whining, legitimate requests to learn, and anything in between. The only real downside is that its sheer scope tempts one to over use it. That too sounds like a skill issue.
IRON NODER XVII: ALL'S FERROUS IN LOVE AND NODING