I have a R1200gs and I can't select neutral when it's running. What do you think the problem might be?

ok- you've got an old honda dual mode transmission. It will start in neutral and will run in gear but you can't transition from neutral to gear-clutch issue,I think its a hydraulic clutch may require slave cylinder or rebuild-first check for clutch plate movement b4 rebuilding-clymers/haynes manual great investment. Next the battery: either the battery is pooched- can't hold charge or the stator/regulator is malfunctioning or has failed and your battery is the only thing powering the bike thus it runs until the battery has been used up, good luck.

No, Diagnostic software cannot measure your clutch wear.

Remove the starter motor. You will be able to see a small section of the clutch and measure the thickness.