I have meditated on this one long myself. I absolutely hate soldering wire to board. I generally don’t like using solid wire (which is easier to solder to boards imho) and I can rarely get stranded wire to fit neatly into a through hole unless it’s like 26 gauge. There’s always a stray strand or two and I go insane.
But more importantly I like keeping offboard wiring as easy to remove from an enclosure / board because it makes troubleshooting so easy. If you combine it with testing potentiometers either in an enclosure or using toothpicks to keep them in place temporarily, its really easy for me to troubleshoot builds.
My answer has been 2.54mm pitch screw terminals, and I use them in every build. I try to use them in 3 places on most boards: the top row of +, -, leds, and in/out grounds, the bottom row of in/ground/switch/out and on the 3pdt breakout board. Some larger boards can prevent it from being feasible to use them on the 3pdt board though. I use 4 pin ribbon wire from the board to footswitch with the screw terminals. Of the connections that can be undone that I've tried in my builds, they feel the most secure by far.
In my opinion the length of the actual connector on dupont/header cables makes them really annoying to use in a 125b. It’s probably possible but they get clunky so fast. And that is before factoring in the length of wire that they usually come in, and hand crimping dupont cable connectors is a special kind of hell that I wouldn’t wish on my worst enemy. They also never feel super secure to me. I’m sure they hold up but they just doesn’t fill me with confidence in the context of a pedal.
I also don’t think jst/xh connectors make a lot of sense, considering that both ends have to be the same number of pins (I think?) The only place in pedalpcb builds that they would make sense is between the footswitch and the bottom of the board where the connections are lined up on both sides and are next to eachother, but then you are stuck with the input and output being wired differently - I’ve never seen a single pin jst connector.
Anyway these are just my thoughts. I’m team screw terminal until I find a better answer, which I’m always looking for.