I have also issues with sixaxis and the galaxy s4. My galaxy S4 is rooted and i can connect with sixaxis. The problem is that the touch emulation profile is not working. No buttons or stick respond in the game.
I tried joystick center 7 and there is the same problem. I am sure it is because the Galaxy S4 has a full HD screen and these applications (sixaxis and joystick center) do not work yet with full hd resolution and the touch emulation is then messed up. We need to wait for an update.
But i have found the only one touch emulation controller that is working right now with the galaxy s4. It is called Gamekeyboard on the google play. It works very well with the ps3 controller (already tried it successfully with dungeon hunter 4 and modern combat 4). The only drawback is that it is very less userfriendly (for me) than sixaxis.