I usually try koreader first, and if zooming is a better solution, I leave the parts to be zoomed, and after reading the parts, which I can read in koreader, I switch to nickel, and finish there. (But I mostly read PDFs made of PPT-s needed for my work, where zoomed, usually tabular information, and textual handled well in koreader are separate.) Actually I like the stock PDF solution also better than the one on my old kindle PW, and I think the nickel and koreader PDF readers are quite good together.
The other thing I did was adjusting margins, it also helps sometimes (if you cut off the complicated parts, handling the simpler parts can be much better).
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