The 9-Speed ZF transmission used in the Cherokee has had it's issues. There have been several software updates that FCA claims address the problems. From the data I've seen it seems the problems are most prevalent on the 2014 models, somewhat less so on the 2015 models. I don't think there is enough data on the 2016's to know for sure whether it's been addressed. There is no doubt there is a history of problems in this area, so be aware. Most of the complaints are things like hard shifting, lunging, warning lights in the dash, and in some cases disengagement of the transmission.
That said, if you look at the overall reliability history from the 2014 and 2015 model years the Cherokee has better reliability than the Grand Cherokee by quite a wide margin, and the reliability of the Cherokee isn't too much different than the Wrangler.
The same transmission is used in the Renegade, the Fiat 500X and the Chrysler 200.
IMO if you really want to be assured of the highest possible reliability you probably should think twice about buying a Jeep, and I say that as someone with a new Cherokee in my driveway.