I managed to get my PS3 pad to work almost perfectly.
I used MotioninJoy as well, then I noticed you cannot diagonally jump with D-pad(works with the left-stick).
Searched Google for a solution but there was none and found some troubling searches where Motionjoy kinda infects your computer with adds and such. So I removed that program, noticed that the drivers are still installed for the controller in device manager. Tried it out and noticed that everything is working except for the thumbsticks(which I don't care for in a fighting game). Tried it out in-game and diagonal jumping was working.
There is one "issue" remaining, the fact that menu uses default controls and certain buttons are switched. X and Circle are switched(your press Circle for OK and Cross to cancel, very confusing at first) + Square and Triangle are switched as well. Which could be solved with the MotioninJoy program by switching the button ID's. But I'd rather have diagonal jumping than switched inputs at the menu.
I'm still searching for a good solution where you don't have to install something first and then uninstall it + where the button mapping is correct.
For the people that want to accept this temporary solution, download
here. Install it and follow a tutorial where you load the driver for your plugged in controller. See if it works in device manager and then delete the program.