In my experience, stock pickups are fine unless you are going for something specific that a particular set of aftermarket pickups has in known quantities beforehand.
For instance, I got a Strandberg Boden OS (made in the same Korean factory as that 2011 SE I'll wager) and had Lace Alumitones put in. I
'm currently pondering having the original Seymour Duncan Jazz and JB put back in. They're a bit warmer. I
knew the Alumitones were going to be bright, but I kinda think they' too bright now.
People have a natural affinity for being down on stock pickups just because of the name 'stock pickups', it sounds so derogatory.
As it turns out those stock pickups can turn out to be really good if you give them a chance. It all depends on what you're plugging them into and how that is set up.... which is the beauty of an Axe-FX II.
You can dial it in any way you want. A lot of people get crazy about pickups when they haven't really learned how to use those little Bass, Mid, Treble and Volume knobs yet.
Not saying you don't, but just live with pickups first, see what characteristics and sounds they have to give you, before you go and blow another $250 on racy pickups.
All of my guitars except for my first guitar (a Charvel/Jackson), a Steinberger Spirit (which is a hunk of junk with a legendary name on it), and the Boden, have stock pickups in them.