The R version for both kit lenses were released together with the new PEN cameras and are supposed to be designed to work together with these cameras in achieving the so-called fastest AF speed in the world.
I believe that optically they are the same as the older versions. The main difference is cosmetic. The new lenses have a nicer looking and updated exterior design. See comparison below (I have both lenses)...
Although it was claimed that they are designed to focus faster with the new PENs, I find that the old version of the 40-150mm focus just as fast as the new one on my EP3... meaning I can't detect any noticeable difference in focusing speed between the 2 lenses.
If you buy the 40-150mm separately, you would get a better lens end-cap instead of the kit lens type of cheapo end-cap for the $100+ price difference though.