Its not such complicated, I used an PI3 with Raspbian Jessie. But Batocera is far more advanced and has as standard this module not in place. So, you have a risk with upgrades, as it will not be automatically upgraded.
I have the compiled module for 4.4, working with Recalbox 18/07/13. I am in general not making promotion for this clan, but the guy who made this build also leaved the sinking ship. I made some other modification as new and far more quick lcd driver in compare to the waveshare. I think for a small handheld this Recalbox version is ok. On PC and other platforms, Batocera is much more advanced. As this people never conserve old versions, I can put you driver and RB 18/07/13 for download.
In recalbox.conf you must define this lines with your gpio data, map=5
------------ D2 - GPIO Controllers ------------
enable controllers on GPIO with mk_arcarde_joystick_rpi (0,1)
mk_gpio arguments, map=1 for one controller, map=1,2 for 2 (map=1,map=1,2)
gpio with button order: Y-,Y+,X-,X+,start,select,a,b,tr,y,x,tl,hk