A few things: The support community for Apex is much better organized and more responsive, and I'm including the manufacturer on that. At a local level (this club) the apex users are legion and willing to help.
At some level, it comes down to Chevy/Ford, Nikon/Canon.
With that in mind,apex has a reputation as being more solid and less prone to tank killing disasters like this one (tried googling "apex tank disaster" and didnt return anything)
http://www.forum.digitalaquatics.com/viewtopic.php?f=4&t=6194
From a technical level, both have various combinations of features that the other does not unless you add expansion modules in (the full apex has 0-10v dimming, the RKE does not BUT the RKE has switch inputs stock, the apex does not). It's going to come down to what you want this to do for you, and how much you want local help.