Base it off of what you want or need it to do...not a bad idea but the problem with that is when you get it figured out you will want to control more. I originally bought the apex jr. I should have read some more before ordering it because it didn't have something that I thought it did. Returned it and got the full apex. Tried it and could never get it working because I have to use wifi and couldn't get the gaming adapter to work properly. Ended up with the new model apex and love it. I originally just wanted to be able to control a few things in event of a power outage (apex is hooked to battery backup). After tons of reading on the Neptune forum, I will soon have everything hooked to 2 EB832s. I still use EcoSmart Live to control my Radions, Vectra, and Vortechs. Not sure if I will take the plunge to the WXM module to control through Apex since everything is working great now. Having things hooked to the energy bar is nice to be able to shut off power for certain conditions and with the 832, be able to monitor power at each outlet. The ALD module will be coming soon to add more peace of mind.
I probably enjoy the technical side of a reef tank as much as I like my livestock, but I am far from an expert. Some of the guys on the Neptune forum have an unbelievable amount of knowledge about the Apex. I've spent hours on there learning about what it is capable of doing.
To sum it up, if you can swing it, go with the new Apex and you won't regret it.