Do you have links on how to use the gpio pins?
There is
GPIONext here or
Retrogame here. I think I like Retrogame a little more just because it does not have hot keys so there is no delay. GPIONext can use hot keys for combo but it has a delay to look for hot key combos. If you do not use the hot keys, then I think they are about the same. I take that back, you can use 1 hot key in Retrogame by assigning two pins to a hot key. They have to both be held down for a couple seconds which helps accidental activation.
The one difference that I did notice is that I could assign two pins to the same key in Retrogame which worked for me because on one machine I had a 4 way and 8 way stick both mapped to up, down, left and right. I would have to wire them daisy chain style to use GPIONext. Which is not a big deal but...
You can use 26 of the pins if you are not using them for something else (I2C or PiTFT or Serial or I2S...not even sure what most of those are).
This page has some good info about the pins you can use.
Let me know if you have questions on either. I think I have a decent enough grasp on both (enough to make them work at least).
J_K_M_A_N