First I decided to switch the highlighting to names instead of the SD/SA/EFF which enables the feature for all powers instead of just those which are tagged with special effects. I think it's a great way to look up keywords/range/etc. Here you see it working on an aura.
And then, because my email contained the phrase: "Now all you have to do is figure out a way for me to mark when encounter powers are used by NPC’s and I’ll be happy forever!"
I decided to see if I couldn't do something with those [e]'s that follow limited usage powers. In the end I made them like [R:#] powers. If you double click on the [e] it toggles to [USED] if you roll/drag an attack clause with a [e], it also clicks to [USED]. The screen shots show examples.