There where a bunch of other people who said games ran smoother on the older versions, I see that you have integrated graphics so if you are trying to run the game at a higher internal resolution setting with AA that might be causing your issue in the newer setting. Otherwise I can't tell you why you have bad fps in the newer version. Maybe you have per pixel lighting turned on? I myself get bad fps with per pixel lighting turned on and I have to drop my SSAAx4 down to AAx4 to maintain a stable 60 fps at 4xir.
Intel i5-4690k @ 4.6 GHz | Gigabyte GTX 970 4GB G1 | 8 GB DDR3 @ 1600 MHz | Windows 10 TP | Dolphin 4.0-6811