Release date usually. I think it makes more sense to do. With Metal Gear Solid 3 as the start of the timeline, you would be starting in a weird place I feel as it's supposed to be about how Big Boss's legend started, but you aren't going to get that same feel starting there compared to the games later on in the timeline, starting with Liquid and Solid in the first game. You play that first and go on from there, learning more, getting this talk about how important Big Boss was and then you finally get to play him.
As for HD versions, I would usually chose the more modern release unless something about it is bad. So I would pick Twin Snakes over the PS1 version. Or Final Fantasy X HD over the PS2 version. Some exceptions would be like Super Mario All-Stars remakes the old NES games in a visually better style, but I would want to play the original versions personally. Sorta depends on the original nature of the game as some don't particularly age super well, such as the visuals on old PS1 games lol
Spinning off of that, I would say it's also because of controls. Metal Gear Solid 1 plays way differently from Metal Gear Solid 4. You get to see how the series progressed. Don't get that as much starting in the timeline.
As someone brought up Star Wars movie wise, if I had to show it someone new, I would always start with the originals over the prequels.