I'm pretty sure you can with the option that says Refresh Rate in the config program.
[attach=1]
(click it to make it more clear, it seems to have inserted badly :derp:)
You should be able to set that to 1/2 or 1/3 for frame skipping, as refresh rate is just another way to say frame skipping, really. (i.e. 1/2 the frames and 1/3 the frames)
EDIT: Actually, you can also put the colors down to 16-bits to improve performance. It'll make it look a little worse, but the fps should go up on older systems since that would be less work for the graphics card. I wouldn't really go messing around with the other settings for EoSD as they really can bork up the game.