The knit fabric that I brought today was a very slinky fabric that gave me fits on my CS6000i. The NQ1300 handled it fine with a narrow zigzag and a straight stitch (that I normally wouldn't use because the stitches would pop upon first wear). The Skyline S5 ate the fabric. The dealer had to cut a hole in the sample to get it out, and this was using the stretch stitch that SHE recommended. She changed the plate out to the straight stitch plate, which worked better. After using the zigzag and straight stitch, it looked very similar to the NQ 1300 (the Brother's stitches looked very slightly better). It seemed to feed smoother through the Brother, and I didn't have to change plates to sew the fabric.
So I switched to a denim piece to try some decorative stitches (as close to what I tried on the NQ1300 as I could). Surprisingly, those stitches were also terrible. They were too sparse and seemed about the same quality as the NQ1300. It was probably just the settings, but I was surprised that the default would look like that. Changing stitches was as easy on the Skyline as it was on the NQ 1300, but there were fewer choices. I did like that the Skyline had a few children's stitches that weren't feminine (car, plane, and house) that I could have used for my nephew.
I ended up buying the NQ1300. While the Skyline S5 was certainly a great machine that I would still be very happy with, the NQ1300 was just better. It handled my worst fabric more easily, had more stitch choices, and the quality of the stitches seemed to be the same. I chose the NQ1300 over the NQ900 to get the auto height adjustment.
One more big selling point was the automatic threader - MUCH better on the Brother. The Skyline has the same threader as the Brother CS6000i - it's just cheaper feeling and I know will wear out after a few months. At least on my CS6000i, it just doesn't line up quite the same after a while. The NQ1300 seems sturdier, but time will tell I guess.
My dealer also gave me $100 off to buy the surplus machine from her class. It was never used (ordered too many), not even threaded they said. Brother is also offering a rolling bag and $50 Visa gift card via rebate. I don't know if the Janome had any rebates, but the dealer special brought the NQ1300 to only $200 more than the S5.