The RK2 is expandable, you can add as many circuits as you want. (It comes with 8 BTW)
I have been using one for close to a year and am very happy with it, no problems at all. One of the nice things about it is that it has upgradable software. Every so often Digital Aquatics will release an update and you plug the controller into your computer and update it... they have had some cool ones, too. I don't think you can do this with the AQ Jr., but I may be mistaken. I have also heard and seen first hand that the temp probes on the AQ can go out, the one I saw read about 25 degrees higher than actual temp.