Gray Area responded to my Kobo post, pointing out, among other things, that you can actually save settings application-wide in KOReader, and not only for a particular book. That motivated me to give it another try, mainly for the sake of better font rendering, and hypenation (the lack of hyphenation in Nickel drives me batty).
So far, so good. I’ve got the defaults the way I want them now.
I mitigated the issue of Calibre making it hard to browse books in KOReader by configuring Calibre to not use subdirectories when sending books to the Kobo. The file browser is still not as good as the Nickel catalog, but it is good enough now.
Another thing I’ve got it to do is to show random images from a folder (of black and white landscape photographs) as the sleep display rather than the cover of the current book; this was something I liked about the Nook Simple Touch.
At some point, I hope to get articles working under KOReader, though I’m not yet sure by what method.