Exclusively using dupont jumpers instead of typical wires for BB computer -- bad idea?

Just kicking off the project and finding wiring to be incredibly time consuming. Manual wiring will obviously look better, but I'm very tempted to go with dupont jumpers since they're plug and play.

That said, there are obviously a lot of wires in this project and I suspect my breadboard will look like spaghetti by the time I'm finished if I don't bundle wires together with zip ties or similar. I also suspect debuggability will suffer, but then again perhaps it will be improved if wires are properly grouped and organized (since it's actually easier to see individual wires when they project into space vs. are squished against the breadboard).

Figured I'd ask before I get too deep into the project.

Bonus question: are folks trimming their components' leads to keep them closer to the breadboard?