It's a Mercedes vs. BMW thing - one is more plush and fuel efficient while the other is sportier and has better handling. So in short, it depends on your particular needs. I have used RKL/RKE over the years and have never used the Apex but based on my readings, both are very good at what they do and there's little differences between the two. For example, the Reefkeeper is easier to set up & program but almost everything needs a separate module; the net module is difficult to set up and it's finicky (some exceptions with the new Archon). The Apex is a little better integrated and has a much larger user base but apparently has a steeper learning curve for it's counter-intuitive menu.
Right now I wish I had an Apex to integrate the control of my Aqua Illumination LEDs which the Reefkeeper is not compatible with but it's not a deal-killer - I have been quite happy with the Reefkeeper. Best advice is keep researching