I'd stick with a paper filter. The air intake on the JL is a really well though-out design that works very well with a good paper filter.
If I were looking for a performance filter, I'd go all out with a Banks Ram Air. But, being an off-road vehicle, as fun as that 3.6 is on the road, I decided to keep mine set up to minimize dust intrusion. I'm currently running Wix filters from Napa. I had one in it for a trip to Moab and it went through a week of horrendous dust on the trail. It was loaded with dirt on the proper side. Not a speck of dust was found on the clean side of the filter or housing. I don't think a cloth filter would have fared so well. It certainly wouldn't have the area of the paper filter or the capacity, let alone the ability to filter as fine a dust.
I doubt you'd gain any noticeable power with the cloth filter, either, unless you did the whole CAI. It might sound pretty cool, though.
Between those two, I'd go cone. I think you are right that it would have more area. I'm sure Afe would tell you the difference.
Just my 2 cents.