The E controller also uses heavier wire (I think), which is good for more power and longer distances, but with only 4AA batteries it probably won't make much difference.
You can replace the wire on your regular controller with 30' of 18 gauge speaker wire very easily, just cut off the old wire and splice on the new one (soldering would be best). Better yet, build your own controller with a better battery, like a NiCd pack or a small lead acid battery.