On a similar vein as this question about Electrocute, will the three Magic Missiles fired by the Split rune trigger the effects of Prodigy for each of the missiles that hits an enemy, or only once per cast?
After some testing it does appear that multiple hits by using the 'Split' rune will trigger multiple effects from the 'Prodigy' passive ability. With this in mind in conjunction with the thread you've linked for Electrocute, I believe it safe to state that the 'Prodigy' passive will proc every single time one of the signature abilities hits. This should mean that the 'Spectral Blades' ability is overpowered for Arcane Power regeneration.
After some further testing with Spectral Blades I can confirm this is actually how the 'Prodigy' passive works (one attack with Spectral Blades on a group of 7 enemies resulted in my Arcane Power going from 'nearly empty' to 'nearly full' in one attack).
My methodology for testing:
What I found:
The 'Prodigy' passive ability does exactly what it says it does. When you deal damage with a Signature ability with the 'Prodigy' passive enabled, you will get 4 Arcane Power per enemy that is damaged during that cast.
This stacks with the equivalent runes on the abilities themselves, so you can use Prodigy + Siphoning Blades, for example.