I own 2 S2's, Custom 22, and a 22 HB(single F hole). both had SE(G&B, gone within the 1st week of ownership) pickups. I also own 4 SE's, a Zack Meyers(greeny mint color), a mid 2000s Santana, a SE Custom 22 HB in whale blue, and a Singlecut in transparent black. I also had a Singlecut with P90s from the early 2000s.
The S2 quality is not that better if at all, but then again, I'm an advanced hobbyist luthier and can fix most of what I don't like.
For example the SEs and S2s both have nuts that need the corners taken down. I use a radius block with 400 grit to shape it to the neck and polish it up afterwards.
These are 2 of my SE's. I put BKP HBP90 Nantucket's with distressed covers in the Zack. The pickups in the HB have been change twice and the picture doesn't reflect the BKP Mules minus the Peter green flip. My mistake was not knowing the Peter green flip require flipping magnets to create an out of phase. OOOPS. gaining knowledge at the expense of ignorance!