Except hook up to the internet, view parameters on a smart phone, control things like lights, etc.. The RKL does come with a pH probe though, something you need to add on to the Apex Jr, but the Apex has ethernet built in, which is quickly becoming the "must have" feature for anyone buying a controller today. Reefkeeper Lite was the best for a budget controller last year, I can't say it still holds the title this year though.
Conski, wanted to mention something off topic, on that last video in Guillo's tank thread, in the middle of the tank, you can see 2 giant Spongodes colonies, that is where the one I gave you came from.