Highlight object groups in keynote
I've built a small demo Keynote file (v5.1, on Mac OS 10.6.8, hope you can open it) -- this does what you're trying to achieve. At start only group 1 is fully opaque, then after each click, group 2 and 3 gain full opacity while the other groups are 50% transparent.
I've solved the 0.1s flicker by putting a copy of the groups underneath group 2 and 3 and setting it to 0% transparency at the beginning.
It could use some tweaking, I'll admit that, but that was just a quick 2am demo.