The "figures that are deliberately placed close to the relevant section in the text" is something I've heard often, and I'd agree to an extent. But the figure is never 10 pages away (unless you have a tiny screen or something). It's easy to put an image inbetween 2 paragraphs. With PDF papers 1 figure is often referenced in several places throughout the paper so I just open 2 windows with the paper anyway.

For justified text - what's the point of stretching each line artificially just so they align at the end? It looks awful to me even when done "correctly". Having uneven spaces makes it harder to read. Having every line align on the right also makes it harder to read. When you have uneven lines, I subconsciously use the different at the end as an anchor for where I am in the text or where a certain phrase was. Hyphenating words is another thing that doesn't make a lot of sense nowadays - we have enough words with a hyphen naturally in them, so reading a broken up word is mentally taxing as I have to figure out if it's a normal word with a hyphen or a broken up one.

All the arXiv HTML papers are much better to read in the browser, IMO. And they'll only get better. PDF will likely stay the same.

For small screens like phones or tablets, having to constantly scroll up and down and left and right for a 2-column paper is just painful. PDF is much better on a big screen.