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Hi Alan,
I must say, I originally installed KOreader for the same reason as you did - I'm looking for a way to store a significant library of scientific PDFs (even though I bought my Kobo reader for personal use, to read novels). In my (short) experience KOreader is way better than Nickel at displaying PDFs, but is still not quite satisfying. I didn't try making very extensive experiments, but for some documents, page clipping didn't work too well, and the end result was that the displayed part was still too small for comfortable reading, even in landscape mode.
If you have good tips on how to configure KOreader, I'm very much interested (or even just a good place for documentation on how to do X or Y with it). My guess is that it can do a lot of things, but you may have to work a little bit on configuration and tuning.
(For regular novels, it seems to me that Nickel is rather more convenient - but then, I'm not using my Kobo reader as a storing medium for novels, so I'm not keeping a huge library on it - which is quite the opposite of what I'd like to do with scientific PDFs)
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