I've actually been debating the same thing for the past two weeks. I can't decide which one to get. If you go with the AquaController Jr I would buy it with the serial port option. You can't add it later and it is useful to download logs, change settings on the device, for use as an I/O port, and to upgrade the firmware. The ReefKeeper 2 has a serial port built in, which is used for software updates and the data log.
AquaController Jr Pros:
- serial port can also be used as an I/O port with a float switch, etc, i could see this useful to implement and auto top off system
- scripting language gives you the ability to shut off devices in response to other parameters such as temp or the io port
- sunrise and sunset stimulation for varied light times based on the seasons
- can control 12 devices however for the price of a DC8 and DC4 you might as well buy two controllers
AquaController Jr Cons:
- DC8 box used triacs only. The ReefKeeper 2 has 2 relay outlets and 6 traics (2 of them spaced for transformers). Some lights have issues with triacs and very small current devices aren't can't be turned off. The DC4 boxes use relays but cost more than the DC 8 box.
- control panel isn't designed as nice with indicator lights per channel
- I/O port can't be used at the same time as the serial port
- X10 has terrible reliability and I wouldn't use it, hardwired boxes get expensive
ReefKeeper 2 Pros:
- design of control panel with status lights per channel
- 2 relays and 6 triac switched outlets (2 of which are transformer spaced)
- manual override of channels
- standy/feed mode to turn of certain devices like the sump to prevent food from being sucked into it
ReekKeeper 2 Cons:
- no scripting language so your limited to hard coded functionality
- only 8 devices can be controlled no expandability
I don't have either one of these controllers so hopefully I am correct on the above info from the research I have done. Somebody can correct me if I'm wrong. I'm leaning towards the AquaController Jr for the scripting language, io port for float switch, and sunrise sunset feature so I don't have to adjust the light times throughout the year. However I like the ReefKeeper 2's ability to manual override channels, for example if I want to turn the lights on to show the tank, and the feed mode as my sump likes to suck down the food. I wish I had the money for the AquaController 3 as it has all the functionality and expandability you could ask for.