KOReader is supposed to be better with handling PDFs, it's also got a directory based system. I only played with it for a very short time but I found it wasn't for me. That's not to say it isn't a good reader, but I wasn't thrilled with the controls. Perhaps if I gave it more time I'd have grown used to it. But I like the default reader app enough that I don't really care to change.
I haven't used cool reader at all.
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