What music are you playing? What do you want out of a pickup? What do you find lacking in the stock ones? High gain/low gain/clean?
There are so many variables that will allow you to choose the right pickups. Not that there is anything inherently "wrong" with the stock S2 pickups, but all I can tell you is that I changed out the pickups in my S2 Mira and I could not be happier with the results. I always think this is one area where you can fine-tune the guitar to your specific needs and get exactly the tone and response you want.
I personally tend to like a pretty hot bridge pickup coupled with a vintage to slightly hotter than vintage neck pickup. In fact, all but one of my two-humbucker guitars follow this layout, with a hot ceramic magnet bridge and an A-2 or A-5 PAF-voiced neck pickup. This works for me into a medium gain amp with minimal effects. I just use a boost and a wah most of the time and I can cover all of the classic/hard rock tones I am looking for.