As far as I can, tell JL axles are becoming much more popular. The downfalls are the FAD and the aluminum knuckle.

if you FB.

 

JLs are a bit stronger and wider but you've got the FAD. I've seen some pretty mild JL/JT builds break things axle wise so for me I'd lean towards trussing JKs.

The pick up points on brackets are also not the same. I believe Artec has a JL to TJ kit in the works.

But the FAD kills it for me.

 

Dana makes a FAD delete kit for the JL axles (it's about $100) or you can get Yukon axle shafts that bypass the FAD with a solid long-side shaft. As far as knuckles, Reid racing makes iron replacement units for about $650 per side. The pickup points are the same on the JK and JL front axle, I'm using a JL M186 (Dana 30) under a JK frame on my YJ build. I can't confirm on the rear though, my M220 was from a Gladiator which is way different.