I also recently bought a S4 and also cannot get Sixaxis or any other controller app to work yet. I've been able to get everything fully working except for the right joy stick.
My S4 is rooted and it seems the only problem I am running into is emulating touch. I've been reading through forum after forum for days now and I haven't found a fix yet. I am starting to get discouraged.
I have tried Modern Combat 4, Real Racing, and Dungeon Hunter 4 with several different PS3 controllers both wired and through BlueTooth so I know mine isn't broken.
I'll let you know if I solve it or find a fix somewhere. I feel your frustration.
Found pre-made profiles here: http://forum.xda-developers.com/showthread.php?t=2035695
I'm going to try them now.