To me, the Core model pickups sound better. More like real early 60's Strat pickups. More authentic. I think they're great.
The SE pickups are really good too, but I hear a very slight, but springy sort of sizzle way up at the top of the treble that kept me from being 100% comfortable with their sound.
But I wanted them to sound like my '63 Strat. A real one.
So I replaced the pickups in my two SE's.
First with Seymour Duncan Antiquity Surfers and then with Chubtones which have a slightly smoother, fatter sound like a '61 Strat.
When I compared the Chubtones to a CORE Silver Sky, the Chubtones were smoother and "woodier" but the CORE SS pickups seemed slightly hotter. Not by much.
Both sounded killer.