I own the ONE and have used the S4 a few times now. It's going to really come down to preference in the long run.
A lot of people like to talk smack about sense and touch wiz, and honestly I really don't like either, I like stock Vanilla...But as we know that's not going to happen right now without some rooting and all that jazz.
Anyway back to what we have on the S4 and ONE. Man you really can't go wrong with either one. I guess the reason I went with the ONE is because its so fresh with a new design, and after owning the S3 before my nexus 4 I just wanted something brand new that felt fresh to me, and the S3 just didn't strike me as that type of phone since it has basically a GS3s design from top to bottom. I know under the hood has been tweaked a lot and reviews have been very positive lately about the S4, I just felt like the ONE gave me something I'd been missing from Android for a while....that wow factor when you pick up the phone.
But I'd say to anyone in the market for a device right now...either is at the top of its game no matter which one you choose. I just hope moving along that this trend with using high grade materials like HTC did for the ONE trickles down to companies like Samsung in the future.