It's really a matter of preference, the Elk has more space limitations. The Elk has a more logical rule engine, but the ISY's is more powerful (IMHO). Assuming you have the Elk module on the ISY, you should be able to do anything on the ISY that you can on the Elk, but not vice versa.
I moved all lighting rules to the ISY and actually don't even bother updating my light info on the Elk anymore. And other than having to figure out the quirks of the ISY rule engine and creating multiple rules where on the Elk there was one, I haven't had any issues.