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Well, PDF, XPS and DJVU viewing is only present in Koreader, I think (that's where it started).
Both readers do the rest of the supported formats, which would be EPUB (to some degree, but pretty usable for what comes across), FB2, TXT, HTML (simple rendering here) and a bunch of others, like PDB (and even old DOC and CHM, I think).
The readers differ in their user interface.
From a developer's viewpoint, they are vastly different when it comes to developing the user interface. For Koreader, that is realized using Lua scripting, Coolreader uses C++ (Qt).
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