I have had experience with both, although not the newest RKE. I do agree with everyone, the RK interface is much simpler then Neptune's. But for my needs, the APEX does the job. And Neptune's interface is really not rocket science like many claim. In a sense, they are now both equalling out since neptune has been rolling out great updates (this applies to the newer APEX JR/APEX). Yes, the APEX is a bit more difficult especially if you want to do fancy things in advanced mode but i think it is a matter of dedication and patience which many of the stories i have heard fall short on.
Again, it will ultimately come down to what needs to be controlled, functions, and price but i will root for Neptune any day. I prefer the integration of functions, interface, and expandability compared to DA.
Now networking will stump most people regardless if it is DA or Neptune. With so many options for interent, routers, access devices, etc. it is a mess to get working for those that have never tackled it.
Keep asking questions, a quality controller makes a difference on one's tank. Good luck, Wiz.