One should be at the bottom one at the top. I understand space on the phone is a premium but a second port would make the phone so much more usable. Wired headphones, flash drives, camera modules, speaker modules, keyboards, even connection to a TV, all could be used while charging. It's a shame it's not a thing, USB is extremely versatile port, but you only get one and it's used for charging half of the time. (I am aware dongles exist)
I agree. If we're going to lose the headphone port in favour of connecting to a universal connection (either directly or via an adaptor) then it's time we have two of them. As for positioning I gather that there are lots of handheld PC's with the one on top and one on bottom configuration and that it's generally accepted to be the best way (and my on top 3.5mm and on bottom USB-c seems to work pretty well) so I think you're right but it would be nice to see manufacturers try out a few different configurations to see in practise what people prefer.
I think on a phone it would make sense for bottom and side, which is the top of a handheld PC. That way you could have the cord sticking out whatever direction was handy for you by turning your phone.
We'll to be clear, on handheld PC's I'm talking about having them on opposite sides rather than at a right angle to each other. But I can definitely see the advantage to the right angle orientation. Personall I prefer to have them in line, yesterday for example I had my phone plugged in to power, with audio out connected via cable and wanted to be able to watch video in landscape orientation. With top and bottom connections it all paid smoothly in a line, had they been at a right-angle then one of them would have had to go straight up into the air out of the middle of the device.
I suspect that right angle is better for flexibility in how to connect a single cable at a time but in line is better for connecting multiple cables at once (really side-by-side is best for multiple at a time but you lose nearly all the flexibility for single cable connection.)