I'm surprised they haven't implemented many of the features that RES has. I certainly don't use RES to it's full extent, but I find several of the features crucial to my Reddit experience.
I hope hope hope they come out with a feature to hide stuff you've already clicked on. I don't get why you'd still want to see something you've already clicked on. At least offer a toggle.
I think that's too personal a preference to make the default, and people would get confused. Imagine someone wanting to show a friend a funny video he found on reddit, and now it's gone.
They have already implemented something similar with the 'hide' button, which allows you to hide a story.
There's a very configurable script for fading seen/hovered/clicked links and it works on multiple sites including Reddit obviously and HN as well. This is more or less right up your alley:
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