What are your future plans that are leading to you doing a DC shaft & SYE? The difference between the normal and the super short SYEs is the length. Super short SYEs shorten the output of the transfer case by about 3 more inches over a normal SYE, which allows for a longer driveshaft and slightly better driveline angles, especially as you lift higher or tummy tuck or anything else that affects the vertical relationship between the transfer case output and rear axle pinion.
There are pros and cons to either kit. The pro to the super short is the length, the con is you get stuck with a tone ring speed sensor which deletes the speedo gear and requires a calibrator to make speedo adjustments. That in and of itself is not a bad thing, calibrators are nice and useful for dialing speed calibration in to how you want it. However, it seems like many people have needed replacement speed sensors from the ones in the kit going bad eventually, and those don't seem all that available. I personally would rather keep the speedo gear setup which I have ultimately found to be the most reliable. So again that brings me to my question of what you're doing with the Jeep that is leading to this change. If you have a medium lift height and no crazy plans for tucking, the standard kit in my mind is a bit more desirable and will still adequately do the job.