I've used the pro version of both launchers for a couple of years. While they both have small differing advantages, I find myself using Apex a little more. Overall I prefer the more polished interface, and currently I find it supports Chronus Widget much better than Nova does. The default layout seems slightly more balanced on Apex too.
I like the multi-app select when setting up Nova way better than Apex's labourious one by one approach, but fortunately you only have to do this the once. Nova also has an extra 3 or 4 transitions.
I haven't noticed any real difference in speed, memory consumption, or battery drain between the two.