One thing I've not seen mentioned, unless I missed it, is geography can play a role in your choice. On the West coast, regular rain is less of a problem and carpet would be my choice. If you leave your jeep open and live in a rainy area, it may not be the best choice. Reason being, factory style carpet retains moisture and allows it to seep through to the floor. It also gets a musty smell pretty rapidly, if left wet. That smell then persists and is difficult to remove.
Since I live in an area that gets pop-up rain showers frequently, and keep my windows out 8 months of the year, I pulled my carpet and replaced it with Bedrug. Of course the tub could have been lined, but I don't like that look. Yes, Bedrug is not the best fitting product, but it solves a problem for those of us that live in wet areas and don't want to look at a lined only tub, or deal with nasty wet carpet. For the bad things mentioned about Bedrug, what it does do extremely well is protect water from seeping through, it doesn't retain water, doesn't mildew or get that funky smell, cleans up easily (mud, dirt, sand, etc.) and looks reasonably well, given the problem it solves.