If you're see what looks like a white screen overlay on the images in your Viewer when running Aperture 3.6 in El Capitan, turn off Onscreen Proofing (View > Onscreen Proofing). This was the case for me after my initial testing on a mid-2012 MacBook Pro 15" running Mac OS X 10.11 and Aperture 3.6.
Here's what happens with Onscreen Proofing turned on (using any of the profiles):
I'll continue to test Aperture 3.6 on El Capitan. So far, this is the first major bug I've found.
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