the biggest defference is that you can access the elite through the internet through a wireless signal. so you can monitor your system through you computer at work or anywhere on the go. here is an excerpt straight from there website:
The ReefKeeper Elite is true to its name, standing alone in the industry as the most innovative aquarium controller on the market. With the most intuitive interface and easy use system controls, you'll find it will simplify all aspects of your aquarium system that it controls. There's also no need to find a power outlet near the head unit as there's no power cord needed; power is provided right from the bus. The compact and convenient design, multiple mounting options and great looks makes the ReefKeeper Elite right for almost any installation; and without any unsightly probe wires dangling about, the head unit will add a touch of class to any tank!
The ReefKeeper is the most expandable controller we know of, allowing the control of over 160 outlets. It has the capability of reading more probes and input devices then even the most demanding system will ever need. All this makes the RK Elite suitable for tanks from 1 to 10000 gallons and beyond.
One of the biggest advantages of the RK Elite system is what it comes with! With other controllers you're left wanting and having to purchase add-ons just to get them to a usable level. The RK Elite system includes two PC4s; that's 8 outlets to control! You also get an SL1 that will allows you to monitor pH, ORP, temperature and two micro switches. Not to mention a free temperature probe and pH probe. All this for hundreds of dollars less than other controllers that barely give you enough to get started.