So I haven't posted in quite some time.. not that I'm even sure that anybody is listening! In case someone is, and like me, you are also running the OS X El Capitan Public Beta and it broke your RubyMotion installation, I provide you this small tip.
After upgrading to El Capitan Public Beta 2 (which I did today), I found that I could no longer run 'motion' from the command-line. Thinking that something broke, I downloaded the RubyMotion installer and re-ran it. I did this on the off chance that the beta had been naughty and broken something.
Alas, reinstallation did nothing. As a workaround (as I'm not 100% sure what has changed between Beta 1 and Beta 2 to cause this behaviour), I suggest adding the following to your .bash_profile (.bash_rc) (assuming you are using bash):