It's largely up to you.
The XD-S by itself should come with two mags and replacement backstraps (maybe they don't anymore?). The Essentials Kit has a bore brush and hard case on top of that.
I wouldn't have any interest in the bore brush and the hard case, so if it were cheaper, I'd just buy the pistol by itself.
Same gun, just different stuff. I'm sure the kit is great for "buying my first gun" guys, not worth much to everybody else.