What’s your GPU mem split like? I was having pretty similar input lag. Upped the GPU’s memory to 256 MB and it seems to have remedied the issue.
Setup (for reference):
Raspberry Pi 2 running Retropie 3.4 from sd image
Class 10 64GB Samsung Evo SD Card
OC’d to Pi2 settings from raspi-config script
256 MB GPU Memory Split
Using Playstation 3 controllers via bluetooth (set up via the retropie-setup script)
Tested on psx, nes and snes libretro emulators (all pertinent settings at their defaults)