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I think my current pet peeve is LaTeX's fixed output. I've been a (La)TeX user for 30+ years, starting off with plain TeX and Knuth's "The TeXbook", followed by Lamport's book on LaTeX. But I wonder whether its day is past. So much of my writing now is read online that I look for publishing solutions that have flexible outputs: the LaTeX -> PDF road, although my go-to for years, simply doesn't cut it any more. People read my stuff online, on computers, tablets, mobile phones of all sorts of sizes and orientations, that a fixed page like PDF has become more of a liability. So I'm moving away from "pure" LaTeX to org-mode with export to HTML, and using MathJax for the equations, and something like JSXGraph for (interactive) diagrams.