I use the ACIII with my chiller and heaters. The ACIII does all sorts of nifty keen stuff. You will also need either a DC8 (direct connect) socket or X10 modules.
The ACJr. is a great way to go, but definitely more expensive. I guess it all depends on how much disposable income you have and what you want to get out of it.
Remember, they aren't mutually exclusive. I bet you could find a way to run both. I am not saying that that is the way to go, but a reefer can never have too many toys or as I explain to my wife, "you can never have too many back-up systems and supplies." I'm not saying that she goes for it, but at least I have an excuse for buying that expensive... (I hope she doesn't read this one)