Personally, I think you're reading a little too far into it, and overanalysing. No offense meant, but we just have to follow the simple rules that Kishimoto has given us, and not try to question or completely understand the logic behind those rules; the rules being "the Sharingan can copy any jutsu with hand seals, excluding blood line abilities". While this rule may not make perfect logical sense, I think we just have to take it with a grain of salt and accept it as part of the story.

Just to throw in my own little part - if you take the example of Itachi vs. Kurenai, when she used her genjutsu on him, he seemed to see what it was straight away and counter it effectively. So in that regard you could say that the Sharingan doesn't only copy jutsus, but it also might see their inner workings and discover an effective counter, all without actually copying the jutsu itself. I don't claim to be coming up with this statement originally, I'm sure it's been said before.