I wish the "Conclusion" section were easier to get to. It's sometimes re-stated in the first/summary paragraph - but I feel like every single time, I have to hunt for the meat of what was found by scrolling down to the conclusion.
In this regard I find medical papers much better than CS ones. The ones in medicine in the abstract write the methodology, the results the CI (confidence interval) and the conclusions.
honestly? the formatting. I know we all love LaTeX and pdfs but reading them on a smartphone is an exercise in frustration. Printing them out isn't great for the planet and my Kindle is the regular size one.
I would love it if authors would put the date the paper was written in the paper itself. I think that's standard for the iacr eprint archive, but sadly missing for many other disciplines.
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Very good abstracts.
I wish papers were written in html or markdown... and the beautiful typography applied later with latex.