The Apple thing only works on 10.10 (which most people reading this wouldn't be using currently), so I am saying that there is an option for earlier systems. Cycript actually doesn't work on 10.10 right now (well, it does, but it is frustrating to use as you have to keep saying this. before global variavles) due to a change made in JacaScriptCore that I am unhappy with (talked to some people at Apple, filed a bug with WebMit, and am checking with a friend of mine on the ECMAScript committee), but I have a reasonable workaround I can use for non-Cydget use and for Cydget crazy one-off Substrate hacks are fair game, so I should have everything fixed soon for a new release.
Will Cycript work on 10.10 or are you just saying that you'll have two JS choices now (Cycript and JS Automation)?
I use Substrate all the time, I really need to look into Cycript! =)