The current Eeschema - ngspice interface has been defined three years ago and has not seen any update since then.
In my view it is a good idea to start a new thread discussing user friendly improvements.
So once I (not being a PCB designer) had the view that one might add an additional layer in Eeschema that allows to encircle a portion of the complete schematic. And only this portion is to be simulated. The circle crossing any interconnect line would cut it. Then either an extra input to this line is to be set or the line allows a measurement, acting as output. This would (hopefully) make different schematics for PCB design and simulation obsolete.
I guess many other, better ideas might surface up, and your inputs are welcome. Solid ideas should then move to the KiCad bug tracker, that now will serve as our input for the developers.
There has already been a detailed entry at https://bugs.launchpad.net/kicad/+bug/1814188