We have an ongoing discussion on that in the topic about a new DS3 driver:
You may want to give this driver a try and remap your controller in Steam Link even if it already is supported - mine was but it had digital triggers, I remapped and triggers became properly analog!
Do note that this may not work for libretro cores just because as far as I can tell, no platform emulated on RetroPie supports analog triggers (L2/R2 buttons were digital on PSX).