Hilariously, I would probably tolerate the HTML version a lot better if it had the font from the PDF (and FWIW, the answer for me is "no: I don't work with LaTeX at all... I just read a lot of papers").
Computer Modern was not designed for easy viewing on screens (think about the screens Knuth would have been using in 1977), it was designed for printing in books.
Two columns is good, albeit annoying on mobile. But the font. The typeface kills me, and almost every LaTeX-generated document sports it.