I was going to suggest the same thing. Whenever someone thinks "nested comments", they have been conditioned to tie nesting level to the amount of indentation. Perhaps a combination of both color changes and much less indentation would work.

Primary comments would be black text on a white background, and as the nesting level increases, the background moves toward black, and text brightness is adjusted for best readability. I've never seen this done, but it might be worth experimenting see more with.