Costs is the biggie! Setting up a 4 link is spendy! Plus getting the geometry correct is another big factor.
Besides leaf springs are awesome! I thought it would be cool to get a LJ and swap in leafs. I have seen a few builds like that. Mostly it would be to with the coil crowd.
Speaking of which, the JK Diesel with the D60 has leafs in the back. They just can't get the load capacity they need with coils.
Then there are those TJ'ers who have switched to rear leafs to get rid of rear steer as well as the squatting and jacking problems. I think Brad Kilby was one of the first to convert the rear coils to Leafs. He also changed the coils to Coil-overs later on. Might as well forget coils and go with a multi-link long arm suspension and coil-overs. Still, that's a lot of work and for most people, overkill.
Leafs are simple technology that works. Problem is most of the complaints of leafs are from mass-produced leafs and not custom ones. When building a custom suspension, you really need to account for YOUR jeeps specs and not someone elses.