The Superlights do sound a little different - snappier, faster response, more controlled low end. The differences aren't big. Nothing that the EQ cannot change.
As for the pickups - I change almost all of mine anyway. Any J style gets EMGs, PJ get EMG PJX, and P stays passive with an Aguilar.
I have the original EMG J set in my Superlight, with an EMG EQ system as well. I love it.